4RKU

Crystal structure of plant Photosystem I at 3 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 ?
  • R-Value Free: 0.293 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of plant Photosystem I at 3.1 Angstrom resolution

Mazor, Y.Borovikova, A.Greenberg, I.Nelson, N.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1721Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05310 (Pisum sativum)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2731Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05311 (Pisum sativum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastic137Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV B, chloroplastic63Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
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UniProt GroupE1C9K6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplastic152Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H2UKZ4 (Pisum sativum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplastic84Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P20120 (Pisum sativum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplastic82Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K9 (Pisum sativum)
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UniProt GroupE1C9K9
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII26Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX40Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaK72Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L3 (Pisum sativum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplastic163Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I-N subunitM [auth N]85Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K7 (Pisum sativum)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6A, chloroplasticN [auth 1]182Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L2 (Pisum sativum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Type II chlorophyll a/b binding protein from photosystem IO [auth 2]199Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticP [auth 3]275Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticQ [auth 4]196Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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XB [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CL0
Query on CL0

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SB [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AD [auth B]
AE [auth G]
AF [auth 1]
AA [auth A],
AB [auth A],
AD [auth B],
AE [auth G],
AF [auth 1],
AG [auth 3],
AH [auth 4],
BA [auth A],
BB [auth A],
BD [auth B],
BE [auth G],
BF [auth 1],
BG [auth 3],
BH [auth 4],
CA [auth A],
CB [auth A],
CD [auth B],
CF [auth 1],
CG [auth 3],
CH [auth 4],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth 1],
DG [auth 3],
DH [auth 4],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth H],
EF [auth 1],
EG [auth 3],
EH [auth 4],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FF [auth 1],
FG [auth 3],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth 1],
GG [auth 3],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth 1],
HG [auth 3],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IG [auth 3],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth 2],
JG [auth 3],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth J],
KF [auth 2],
KG [auth 3],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth J],
LF [auth 2],
LG [auth 3],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth J],
MF [auth 2],
MG [auth 3],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NF [auth 2],
NG [auth 3],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth 2],
OG [auth 3],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth L],
PF [auth 2],
PG [auth 3],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth L],
QF [auth 2],
QG [auth 4],
RA [auth A],
RC [auth B],
RD [auth B],
RE [auth L],
RF [auth 2],
RG [auth 4],
SA [auth A],
SC [auth B],
SD [auth B],
SF [auth 2],
SG [auth 4],
TA [auth A],
TB [auth A],
TC [auth B],
TF [auth 2],
TG [auth 4],
UA [auth A],
UB [auth A],
UC [auth B],
UE [auth 1],
UF [auth 2],
UG [auth 4],
VA [auth A],
VC [auth B],
VE [auth 1],
VF [auth 2],
VG [auth 4],
WA [auth A],
WC [auth B],
WE [auth 1],
WF [auth 2],
WG [auth 4],
XA [auth A],
XC [auth B],
XD [auth F],
XE [auth 1],
XG [auth 4],
YA [auth A],
YC [auth B],
YD [auth F],
YE [auth 1],
YG [auth 4],
ZA [auth A],
ZC [auth B],
ZD [auth F],
ZE [auth 1],
ZG [auth 4]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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DE [auth G],
JE [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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IF [auth 1],
WB [auth B],
Y [auth A],
Z [auth A],
ZF [auth 2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX
Query on NEX

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HH [auth 4](1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
LUT
Query on LUT

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FH [auth 4]
GH [auth 4]
SE [auth 1]
TE [auth 1]
XF [auth 2]
FH [auth 4],
GH [auth 4],
SE [auth 1],
TE [auth 1],
XF [auth 2],
YF [auth 2]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

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AC [auth B]
BC [auth B]
CC [auth B]
CE [auth G]
DC [auth B]
AC [auth B],
BC [auth B],
CC [auth B],
CE [auth G],
DC [auth B],
FE [auth I],
GE [auth I],
HE [auth J],
IE [auth J],
NE [auth L],
OE [auth L],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
VD [auth F],
W [auth A],
WD [auth F],
X [auth A],
YB [auth B],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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R [auth A],
VB [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
RB [auth A],
TD [auth C],
UD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
G3P
Query on G3P

Download Ideal Coordinates CCD File 
IH [auth 4]SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 ?
  • R-Value Free: 0.293 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: P 1 21 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 120.631¦Á = 90
b = 189.168¦Â = 91.11
c = 129.667¦Ã = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 2.0: 2024-11-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
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