8C6K

Double mutant A(L53)C/I(L64)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

PDB DOI: https://doi.org/10.2210/pdb8C6K/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cereibacter sphaeroides 2.4.1
Expression System: Cereibacter sphaeroides 2.4.1
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2023-01-12 Released: 2023-11-22
Deposition Author(s): Gabdulkhakov, A., Selikhanov, G., Fufina, T., Vasilieva, L., Atamas, A., Uhimchuk, D.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.86 Å
R-Value Free: 0.279
R-Value Work: 0.229
R-Value Observed: 0.231

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds.

Selikhanov, G., Atamas, A., Yukhimchuk, D., Fufina, T., Vasilieva, L., Gabdulkhakov, A.

(2023) Membranes (Basel) 13

PubMed: 36837657 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/membranes13020154
Primary Citation of Related Structures:
8C5X, 8C6K, 8C7C, 8C87, 8C88

PubMed Abstract:
The photosynthetic reaction center of the purple nonsulfur bacterium Cereibacter sphaeroides is a useful model for the study of mechanisms of photoinduced electron transfer and a promising component for photo-bio-electrocatalytic systems. The basic research and technological applications of this membrane pigment-protein complex require effective approaches to increase its structural stability. In this work, a rational design approach to genetically modify the reaction centers by introducing disulfide bonds is used. This resulted in significantly increasing the thermal stability of some of the mutant pigment-protein complexes. The formation of the S-S bonds was confirmed by X-ray crystallography as well as SDS-PAGE, and the optical properties of the reaction centers were studied. The genetically modified reaction centers presented here preserved their ability for photochemical charge separation and could be of interest for basic science and biotechnology.

Organizational Affiliation

Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russia.

Macromolecule Content

Total Structure Weight: 103.47 kDa
Atom Count: 7,463
Modelled Residue Count: 823
Deposited Residue Count: 826
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 H chain	A [auth H]	242	Cereibacter sphaeroides 2.4.1	Mutation(s): 0 Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for Q3J170 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J170 Go to UniProtKB: Q3J170
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3J170
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 L chain	B [auth L]	281	Cereibacter sphaeroides 2.4.1	Mutation(s): 2 Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for Q3J1A5 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J1A5 Go to UniProtKB: Q3J1A5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3J1A5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	303	Cereibacter sphaeroides 2.4.1	Mutation(s): 0 Gene Names: pufM Membrane Entity: Yes
UniProt
Find proteins for Q3J1A6 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J1A6 Go to UniProtKB: Q3J1A6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3J1A6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain AA [auth M] MOL2 format, chain AA [auth M] mmCIF format, chain AA [auth M]	AA [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain AA [auth M] Interactions & Density Focus chain AA [auth M]
BCL (Subject of Investigation/LOI) Query on BCL Download Ideal Coordinates CCD File SDF format, chain BA [auth M] SDF format, chain CA [auth M] SDF format, chain O [auth L] SDF format, chain P [auth L] MOL2 format, chain BA [auth M] MOL2 format, chain CA [auth M] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] mmCIF format, chain BA [auth M] mmCIF format, chain CA [auth M] mmCIF format, chain O [auth L] mmCIF format, chain P [auth L]	BA [auth M], CA [auth M], O [auth L], P [auth L]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain BA [auth M] Focus chain CA [auth M] Focus chain O [auth L] Focus chain P [auth L] Interactions & Density Focus chain BA [auth M] Focus chain CA [auth M] Focus chain O [auth L] Focus chain P [auth L]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain DA [auth M] SDF format, chain Q [auth L] MOL2 format, chain DA [auth M] MOL2 format, chain Q [auth L] mmCIF format, chain DA [auth M] mmCIF format, chain Q [auth L]	DA [auth M], Q [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain DA [auth M] Focus chain Q [auth L] Interactions & Density Focus chain DA [auth M] Focus chain Q [auth L]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain FA [auth M] SDF format, chain R [auth L] MOL2 format, chain FA [auth M] MOL2 format, chain R [auth L] mmCIF format, chain FA [auth M] mmCIF format, chain R [auth L]	FA [auth M], R [auth L]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain FA [auth M] Focus chain R [auth L] Interactions & Density Focus chain FA [auth M] Focus chain R [auth L]
SPN (Subject of Investigation/LOI) Query on SPN Download Ideal Coordinates CCD File SDF format, chain GA [auth M] MOL2 format, chain GA [auth M] mmCIF format, chain GA [auth M]	GA [auth M]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain GA [auth M] Interactions & Density Focus chain GA [auth M]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain HA [auth M] SDF format, chain IA [auth M] SDF format, chain JA [auth M] SDF format, chain KA [auth M] SDF format, chain RA [auth M] MOL2 format, chain D [auth H] MOL2 format, chain HA [auth M] MOL2 format, chain IA [auth M] MOL2 format, chain JA [auth M] MOL2 format, chain KA [auth M] MOL2 format, chain RA [auth M] mmCIF format, chain D [auth H] mmCIF format, chain HA [auth M] mmCIF format, chain IA [auth M] mmCIF format, chain JA [auth M] mmCIF format, chain KA [auth M] mmCIF format, chain RA [auth M]	D [auth H] HA [auth M] IA [auth M] JA [auth M] KA [auth M] D [auth H], HA [auth M], IA [auth M], JA [auth M], KA [auth M], RA [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain HA [auth M] Focus chain IA [auth M] Focus chain JA [auth M] Focus chain KA [auth M] Focus chain RA [auth M] Interactions & Density Focus chain D [auth H] Focus chain HA [auth M] Focus chain IA [auth M] Focus chain JA [auth M] Focus chain KA [auth M] Focus chain RA [auth M]
HTO Query on HTO Download Ideal Coordinates CCD File SDF format, chain Y [auth L] SDF format, chain Z [auth L] MOL2 format, chain Y [auth L] MOL2 format, chain Z [auth L] mmCIF format, chain Y [auth L] mmCIF format, chain Z [auth L]	Y [auth L], Z [auth L]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain Y [auth L] Focus chain Z [auth L] Interactions & Density Focus chain Y [auth L] Focus chain Z [auth L]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain NA [auth M] SDF format, chain OA [auth M] MOL2 format, chain I [auth H] MOL2 format, chain NA [auth M] MOL2 format, chain OA [auth M] mmCIF format, chain I [auth H] mmCIF format, chain NA [auth M] mmCIF format, chain OA [auth M]	I [auth H], NA [auth M], OA [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth H] Focus chain NA [auth M] Focus chain OA [auth M] Interactions & Density Focus chain I [auth H] Focus chain NA [auth M] Focus chain OA [auth M]
DIO Query on DIO Download Ideal Coordinates CCD File SDF format, chain W [auth L] MOL2 format, chain W [auth L] mmCIF format, chain W [auth L]	W [auth L]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain W [auth L] Interactions & Density Focus chain W [auth L]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain PA [auth M] SDF format, chain QA [auth M] SDF format, chain X [auth L] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain PA [auth M] MOL2 format, chain QA [auth M] MOL2 format, chain X [auth L] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain PA [auth M] mmCIF format, chain QA [auth M] mmCIF format, chain X [auth L]	J [auth H] K [auth H] L [auth H] M [auth H] PA [auth M] J [auth H], K [auth H], L [auth H], M [auth H], PA [auth M], QA [auth M], X [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain X [auth L] Interactions & Density Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain X [auth L]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain EA [auth M] MOL2 format, chain EA [auth M] mmCIF format, chain EA [auth M]	EA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain EA [auth M] Interactions & Density Focus chain EA [auth M]
K Query on K Download Ideal Coordinates CCD File SDF format, chain N [auth H] MOL2 format, chain N [auth H] mmCIF format, chain N [auth H]	N [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain N [auth H] Interactions & Density Focus chain N [auth H]
UNL Query on UNL Download Ideal Coordinates CCD File	E [auth H] F [auth H] G [auth H] H LA [auth M] E [auth H], F [auth H], G [auth H], H, LA [auth M], MA [auth M], S [auth L], T [auth L], U [auth L], V [auth L]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain LA [auth M] Focus chain MA [auth M] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain LA [auth M] Focus chain MA [auth M] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L] Focus chain V [auth L]