6HQB

Monomeric cyanobacterial photosystem I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Photosystem I Monomer From Synechocystis PCC 6803.

Netzer-El, S.Y.Caspy, I.Nelson, N.

(2018) Front Plant Sci 9: 1865-1865


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A1
A
751Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaA
EC: 1.97.1.12
Find proteins for P29254 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P29254
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A2
B
731Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaB
EC: 1.97.1.12
Find proteins for P29255 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P29255
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem I iron-sulfur center
C
80Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaC
EC: 1.97.1.12
Find proteins for P32422 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P32422
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit II
D
141Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaD
Find proteins for P19569 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P19569
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IV
E
69Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaE
Find proteins for P12975 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P12975
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit III
F
143Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaF
Find proteins for P29256 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P29256
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit VIII
I
40Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaI
Find proteins for Q55330 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  Q55330
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IX
J
40Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaJ
Find proteins for Q55329 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  Q55329
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit PsaK 2
K
70Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaK2
Find proteins for P74564 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P74564
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XI
L
137Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaL
Find proteins for P37277 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P37277
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit XII
M
31Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: psaM
Find proteins for P72986 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P72986
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
A, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SQD
Query on SQD

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Download CCD File 
B, F
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
PQN
Query on PQN

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Download CCD File 
A, B
PHYLLOQUINONE
VITAMIN K1; 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
EQ3
Query on EQ3

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Download CCD File 
I
(3'R)-3'-hydroxy-beta,beta-caroten-4-one
3'-Hydroxyechinenone, 3'-OH-Echinenone
C40 H54 O2
ZRCXVNZZDQGBQT-BANQPSJHSA-N
 Ligand Interaction
ECH
Query on ECH

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Download CCD File 
B, M
beta,beta-caroten-4-one
echinenone
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
 Ligand Interaction
CLA
Query on CLA

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Download CCD File 
A, B, F, J, K, L
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
C7Z
Query on C7Z

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Download CCD File 
F, J
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
C40 H56 O2
JKQXZKUSFCKOGQ-ANDPMPNWSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LMG
Query on LMG

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Download CCD File 
B
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
45D
Query on 45D

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Download CCD File 
B
beta,beta-carotene-4,4'-dione
Isomer of Canthaxanthin
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N
 Ligand Interaction
BCR
Query on BCR

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Download CCD File 
A, B, F, I, J, K
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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Download CCD File 
F
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
LHG
Query on LHG

Download SDF File 
Download CCD File 
A, B
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 124.322α = 90.00
b = 178.658β = 90.00
c = 181.446γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium293579

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Database references