1JB0

Crystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna System from Cyanobacteria

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Three-dimensional Structure of Cyanobacterial Photosystem I at 2.5 A Resolution

Jordan, P., Fromme, P., Witt, H.T., Klukas, O., Saenger, W., Krauss, N.

(2001) Nature 411: 909-917

  • DOI: https://doi.org/10.1038/35082000
  • Primary Citation of Related Structures:  
    1JB0

  • PubMed Abstract: 

    Life on Earth depends on photosynthesis, the conversion of light energy from the Sun to chemical energy. In plants, green algae and cyanobacteria, this process is driven by the cooperation of two large protein-cofactor complexes, photosystems I and II, which are located in the thylakoid photosynthetic membranes. The crystal structure of photosystem I from the thermophilic cyanobacterium Synechococcus elongatus described here provides a picture at atomic detail of 12 protein subunits and 127 cofactors comprising 96 chlorophylls, 2 phylloquinones, 3 Fe4S4 clusters, 22 carotenoids, 4 lipids, a putative Ca2+ ion and 201 water molecules. The structural information on the proteins and cofactors and their interactions provides a basis for understanding how the high efficiency of photosystem I in light capturing and electron transfer is achieved.

    • Organizational Affiliation: 

    Institut für Chemie/Kristallographie, Freie Universität Berlin, D-14195 Berlin, Takustrasse 6, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1755Synechococcus elongatusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2740Synechococcus elongatusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I IRON-SULFUR CENTER80Synechococcus elongatusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II138Synechococcus elongatusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV75Synechococcus elongatusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III164Synechococcus elongatusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIIIG [auth I]38Synechococcus elongatusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IXH [auth J]41Synechococcus elongatusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI [auth K]83Synechococcus elongatusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XIJ [auth L]154Synechococcus elongatusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XIIK [auth M]31Synechococcus elongatusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I SUBUNIT PSAXL [auth X]35Synechococcus elongatusMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA
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AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth K]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth K],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth L],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth L],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth L],
FA [auth A],
FB [auth A],
FC [auth B],
GA [auth A],
GC [auth B],
HA [auth A],
HC [auth B],
HE [auth M],
IA [auth A],
IC [auth B],
JA [auth A],
JC [auth B],
JE [auth X],
KA [auth A],
KC [auth B],
LA [auth A],
LC [auth B],
M [auth A],
MA [auth A],
MC [auth B],
N [auth A],
NA [auth A],
NC [auth B],
O [auth A],
OA [auth A],
OC [auth B],
P [auth A],
PA [auth A],
PC [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RD [auth F],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VD [auth J],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WD [auth J],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG
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ND [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
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OB [auth A],
OD [auth B],
PB [auth A]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR
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FE [auth L]
GD [auth B]
GE [auth L]
HD [auth B]
IB [auth A]
FE [auth L],
GD [auth B],
GE [auth L],
HD [auth B],
IB [auth A],
ID [auth B],
IE [auth M],
JB [auth A],
JD [auth B],
KB [auth A],
KD [auth B],
LB [auth A],
LD [auth B],
MB [auth A],
MD [auth B],
NB [auth A],
SD [auth F],
TD [auth I],
UD [auth I],
XD [auth J],
YD [auth J],
ZD [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN
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FD [auth B],
GB [auth A]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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HB [auth A],
PD [auth C],
QD [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA
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BE [auth L]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 281α = 90
b = 281β = 90
c = 165.2γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2012-07-25
    Changes: Non-polymer description
  • Version 1.4: 2016-05-11
    Changes: Derived calculations
  • Version 1.5: 2018-01-24
    Changes: Database references
  • Version 1.6: 2019-11-20
    Changes: Advisory, Database references, Derived calculations
  • Version 2.0: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary