3I4D

Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1

PDB DOI: https://doi.org/10.2210/pdb3I4D/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Cereibacter sphaeroides
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2009-07-01 Released: 2010-12-01
Deposition Author(s): Fujii, R., Adachi, S., Roszak, A.W., Gardiner, A.T., Cogdell, R.J., Isaacs, N.W., Koshihara, S., Hashimoto, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.207
R-Value Work: 0.181
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of the carotenoid bound to the reaction centre from Rhodobacter sphaeroides 2.4.1 revealed by time-resolved X-ray crystallography

Fujii, R., Adachi, S., Roszak, A.W., Gardiner, A.T., Cogdell, R.J., Isaacs, N.W., Koshihara, S., Hashimoto, H.

To be published.

Macromolecule Content

Total Structure Weight: 111.82 kDa
Atom Count: 8,406
Modelled Residue Count: 822
Deposited Residue Count: 848
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	A [auth L]	281	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides) Explore P0C0Y8 Go to UniProtKB: P0C0Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	B [auth M]	307	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides) Explore P0C0Y9 Go to UniProtKB: P0C0Y9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	C [auth H]	260	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7 Go to UniProtKB: P0C0Y7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain BB [auth M] MOL2 format, chain BB [auth M] mmCIF format, chain BB [auth M]	BB [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BB [auth M] Interactions & Density Focus chain BB [auth M]
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain MA [auth M] SDF format, chain NA [auth M] SDF format, chain E [auth L] MOL2 format, chain D [auth L] MOL2 format, chain MA [auth M] MOL2 format, chain NA [auth M] MOL2 format, chain E [auth L] mmCIF format, chain D [auth L] mmCIF format, chain MA [auth M] mmCIF format, chain NA [auth M] mmCIF format, chain E [auth L]	D [auth L], E [auth L], MA [auth M], NA [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain MA [auth M] Focus chain NA [auth M] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain MA [auth M] Focus chain NA [auth M]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain OA [auth M] MOL2 format, chain F [auth L] MOL2 format, chain OA [auth M] mmCIF format, chain F [auth L] mmCIF format, chain OA [auth M]	F [auth L], OA [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain F [auth L] Focus chain OA [auth M] Interactions & Density Focus chain F [auth L] Focus chain OA [auth M]
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain QA [auth M] MOL2 format, chain G [auth L] MOL2 format, chain QA [auth M] mmCIF format, chain G [auth L] mmCIF format, chain QA [auth M]	G [auth L], QA [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain G [auth L] Focus chain QA [auth M] Interactions & Density Focus chain G [auth L] Focus chain QA [auth M]
SPO Query on SPO Download Ideal Coordinates CCD File SDF format, chain RA [auth M] MOL2 format, chain RA [auth M] mmCIF format, chain RA [auth M]	RA [auth M]	SPHEROIDENE C₄₁ H₆₀ O FJOCMTHZSURUFA-KXCOHNEYSA-N		Interactions Focus chain RA [auth M] Interactions & Density Focus chain RA [auth M]
UQ1 Query on UQ1 Download Ideal Coordinates CCD File SDF format, chain H [auth L] MOL2 format, chain H [auth L] mmCIF format, chain H [auth L]	H [auth L]	UBIQUINONE-1 C₁₄ H₁₈ O₄ SOECUQMRSRVZQQ-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Interactions & Density Focus chain H [auth L]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain BA [auth L] SDF format, chain CA [auth L] SDF format, chain CB [auth M] SDF format, chain DB [auth M] SDF format, chain EA [auth L] SDF format, chain GA [auth L] SDF format, chain HB [auth M] SDF format, chain IA [auth L] SDF format, chain JA [auth L] SDF format, chain KA [auth L] SDF format, chain LA [auth L] SDF format, chain UB [auth H] SDF format, chain VB [auth H] SDF format, chain XB [auth H] SDF format, chain DA [auth L] SDF format, chain EB [auth M] SDF format, chain FA [auth L] SDF format, chain FB [auth M] SDF format, chain GB [auth M] SDF format, chain HA [auth L] SDF format, chain WB [auth H] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth L] MOL2 format, chain CB [auth M] MOL2 format, chain DB [auth M] MOL2 format, chain EA [auth L] MOL2 format, chain GA [auth L] MOL2 format, chain HB [auth M] MOL2 format, chain IA [auth L] MOL2 format, chain JA [auth L] MOL2 format, chain KA [auth L] MOL2 format, chain LA [auth L] MOL2 format, chain UB [auth H] MOL2 format, chain VB [auth H] MOL2 format, chain XB [auth H] MOL2 format, chain DA [auth L] MOL2 format, chain EB [auth M] MOL2 format, chain FA [auth L] MOL2 format, chain FB [auth M] MOL2 format, chain GB [auth M] MOL2 format, chain HA [auth L] MOL2 format, chain WB [auth H] mmCIF format, chain BA [auth L] mmCIF format, chain CA [auth L] mmCIF format, chain CB [auth M] mmCIF format, chain DB [auth M] mmCIF format, chain EA [auth L] mmCIF format, chain GA [auth L] mmCIF format, chain HB [auth M] mmCIF format, chain IA [auth L] mmCIF format, chain JA [auth L] mmCIF format, chain KA [auth L] mmCIF format, chain LA [auth L] mmCIF format, chain UB [auth H] mmCIF format, chain VB [auth H] mmCIF format, chain XB [auth H] mmCIF format, chain DA [auth L] mmCIF format, chain EB [auth M] mmCIF format, chain FA [auth L] mmCIF format, chain FB [auth M] mmCIF format, chain GB [auth M] mmCIF format, chain HA [auth L] mmCIF format, chain WB [auth H]	BA [auth L] CA [auth L] CB [auth M] DA [auth L] DB [auth M] BA [auth L], CA [auth L], CB [auth M], DA [auth L], DB [auth M], EA [auth L], EB [auth M], FA [auth L], FB [auth M], GA [auth L], GB [auth M], HA [auth L], HB [auth M], IA [auth L], JA [auth L], KA [auth L], LA [auth L], UB [auth H], VB [auth H], WB [auth H], XB [auth H]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain BA [auth L] Focus chain CA [auth L] Focus chain CB [auth M] Focus chain DA [auth L] Focus chain DB [auth M] Focus chain EA [auth L] Focus chain EB [auth M] Focus chain FA [auth L] Focus chain FB [auth M] Focus chain GA [auth L] Focus chain GB [auth M] Focus chain HA [auth L] Focus chain HB [auth M] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain UB [auth H] Focus chain VB [auth H] Focus chain WB [auth H] Focus chain XB [auth H] Interactions & Density Focus chain BA [auth L] Focus chain CA [auth L] Focus chain CB [auth M] Focus chain DA [auth L] Focus chain DB [auth M] Focus chain EA [auth L] Focus chain EB [auth M] Focus chain FA [auth L] Focus chain FB [auth M] Focus chain GA [auth L] Focus chain GB [auth M] Focus chain HA [auth L] Focus chain HB [auth M] Focus chain IA [auth L] Focus chain JA [auth L] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain UB [auth H] Focus chain VB [auth H] Focus chain WB [auth H] Focus chain XB [auth H]
HTO Query on HTO Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain TB [auth H] MOL2 format, chain AA [auth L] MOL2 format, chain TB [auth H] mmCIF format, chain AA [auth L] mmCIF format, chain TB [auth H]	AA [auth L], TB [auth H]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain AA [auth L] Focus chain TB [auth H] Interactions & Density Focus chain AA [auth L] Focus chain TB [auth H]
HT3 Query on HT3 Download Ideal Coordinates CCD File SDF format, chain Z [auth L] MOL2 format, chain Z [auth L] mmCIF format, chain Z [auth L]	Z [auth L]	(2R,3S)-heptane-1,2,3-triol C₇ H₁₆ O₃ HXYCHJFUBNTKQR-NKWVEPMBSA-N		Interactions Focus chain Z [auth L] Interactions & Density Focus chain Z [auth L]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain K [auth L] SDF format, chain UA [auth M] SDF format, chain VA [auth M] SDF format, chain J [auth L] SDF format, chain JB [auth H] SDF format, chain L MOL2 format, chain I [auth L] MOL2 format, chain K [auth L] MOL2 format, chain UA [auth M] MOL2 format, chain VA [auth M] MOL2 format, chain J [auth L] MOL2 format, chain JB [auth H] MOL2 format, chain L mmCIF format, chain I [auth L] mmCIF format, chain K [auth L] mmCIF format, chain UA [auth M] mmCIF format, chain VA [auth M] mmCIF format, chain J [auth L] mmCIF format, chain JB [auth H] mmCIF format, chain L	I [auth L] J [auth L] JB [auth H] K [auth L] L I [auth L], J [auth L], JB [auth H], K [auth L], L, UA [auth M], VA [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth L] Focus chain J [auth L] Focus chain JB [auth H] Focus chain K [auth L] Focus chain L Focus chain UA [auth M] Focus chain VA [auth M] Interactions & Density Focus chain I [auth L] Focus chain J [auth L] Focus chain JB [auth H] Focus chain K [auth L] Focus chain L Focus chain UA [auth M] Focus chain VA [auth M]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth M] SDF format, chain KB [auth H] SDF format, chain LB [auth H] SDF format, chain MB [auth H] SDF format, chain NB [auth H] SDF format, chain O [auth L] SDF format, chain OB [auth H] SDF format, chain P [auth L] SDF format, chain PB [auth H] SDF format, chain Q [auth L] SDF format, chain QB [auth H] SDF format, chain R [auth L] SDF format, chain S [auth L] SDF format, chain SB [auth H] SDF format, chain U [auth L] SDF format, chain W [auth L] SDF format, chain WA [auth M] SDF format, chain X [auth L] SDF format, chain XA [auth M] SDF format, chain Y [auth L] SDF format, chain YA [auth M] SDF format, chain ZA [auth M] SDF format, chain N [auth L] SDF format, chain RB [auth H] SDF format, chain T [auth L] SDF format, chain V [auth L] MOL2 format, chain AB [auth M] MOL2 format, chain KB [auth H] MOL2 format, chain LB [auth H] MOL2 format, chain MB [auth H] MOL2 format, chain NB [auth H] MOL2 format, chain O [auth L] MOL2 format, chain OB [auth H] MOL2 format, chain P [auth L] MOL2 format, chain PB [auth H] MOL2 format, chain Q [auth L] MOL2 format, chain QB [auth H] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] MOL2 format, chain SB [auth H] MOL2 format, chain U [auth L] MOL2 format, chain W [auth L] MOL2 format, chain WA [auth M] MOL2 format, chain X [auth L] MOL2 format, chain XA [auth M] MOL2 format, chain Y [auth L] MOL2 format, chain YA [auth M] MOL2 format, chain ZA [auth M] MOL2 format, chain N [auth L] MOL2 format, chain RB [auth H] MOL2 format, chain T [auth L] MOL2 format, chain V [auth L] mmCIF format, chain AB [auth M] mmCIF format, chain KB [auth H] mmCIF format, chain LB [auth H] mmCIF format, chain MB [auth H] mmCIF format, chain NB [auth H] mmCIF format, chain O [auth L] mmCIF format, chain OB [auth H] mmCIF format, chain P [auth L] mmCIF format, chain PB [auth H] mmCIF format, chain Q [auth L] mmCIF format, chain QB [auth H] mmCIF format, chain R [auth L] mmCIF format, chain S [auth L] mmCIF format, chain SB [auth H] mmCIF format, chain U [auth L] mmCIF format, chain W [auth L] mmCIF format, chain WA [auth M] mmCIF format, chain X [auth L] mmCIF format, chain XA [auth M] mmCIF format, chain Y [auth L] mmCIF format, chain YA [auth M] mmCIF format, chain ZA [auth M] mmCIF format, chain N [auth L] mmCIF format, chain RB [auth H] mmCIF format, chain T [auth L] mmCIF format, chain V [auth L]	AB [auth M] KB [auth H] LB [auth H] MB [auth H] N [auth L] AB [auth M], KB [auth H], LB [auth H], MB [auth H], N [auth L], NB [auth H], O [auth L], OB [auth H], P [auth L], PB [auth H], Q [auth L], QB [auth H], R [auth L], RB [auth H], S [auth L], SB [auth H], T [auth L], U [auth L], V [auth L], W [auth L], WA [auth M], X [auth L], XA [auth M], Y [auth L], YA [auth M], ZA [auth M]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth M] Focus chain KB [auth H] Focus chain LB [auth H] Focus chain MB [auth H] Focus chain N [auth L] Focus chain NB [auth H] Focus chain O [auth L] Focus chain OB [auth H] Focus chain P [auth L] Focus chain PB [auth H] Focus chain Q [auth L] Focus chain QB [auth H] Focus chain R [auth L] Focus chain RB [auth H] Focus chain S [auth L] Focus chain SB [auth H] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain WA [auth M] Focus chain X [auth L] Focus chain XA [auth M] Focus chain Y [auth L] Focus chain YA [auth M] Focus chain ZA [auth M] Interactions & Density Focus chain AB [auth M] Focus chain KB [auth H] Focus chain LB [auth H] Focus chain MB [auth H] Focus chain N [auth L] Focus chain NB [auth H] Focus chain O [auth L] Focus chain OB [auth H] Focus chain P [auth L] Focus chain PB [auth H] Focus chain Q [auth L] Focus chain QB [auth H] Focus chain R [auth L] Focus chain RB [auth H] Focus chain S [auth L] Focus chain SB [auth H] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain WA [auth M] Focus chain X [auth L] Focus chain XA [auth M] Focus chain Y [auth L] Focus chain YA [auth M] Focus chain ZA [auth M]
DIO Query on DIO Download Ideal Coordinates CCD File SDF format, chain M [auth L] MOL2 format, chain M [auth L] mmCIF format, chain M [auth L]	M [auth L]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain PA [auth M] MOL2 format, chain PA [auth M] mmCIF format, chain PA [auth M]	PA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain PA [auth M] Interactions & Density Focus chain PA [auth M]
K Query on K Download Ideal Coordinates CCD File SDF format, chain IB [auth H] SDF format, chain SA [auth M] MOL2 format, chain IB [auth H] MOL2 format, chain SA [auth M] mmCIF format, chain IB [auth H] mmCIF format, chain SA [auth M]	IB [auth H], SA [auth M]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain IB [auth H] Focus chain SA [auth M] Interactions & Density Focus chain IB [auth H] Focus chain SA [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain TA [auth M] MOL2 format, chain TA [auth M] mmCIF format, chain TA [auth M]	TA [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain TA [auth M] Interactions & Density Focus chain TA [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.207
R-Value Work: 0.181
R-Value Observed: 0.181
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.8	α = 90
b = 138.8	β = 90
c = 184.569	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations