6HQB | pdb_00006hqb

Monomeric cyanobacterial photosystem I

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 
    0.295 (Depositor), 0.296 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 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

  • DOI: https://doi.org/10.3389/fpls.2018.01865
  • Primary Citation Related Structures: 
    6HQB

  • PubMed Abstract: 

    A single histidine addition to the C-terminus of PsaL of Synechocystis sp. PCC 6803 was previously reported by our lab to shift the trimer-to-monomer ratio of PSI in favor of the monomeric form. P700 re-reduction and NADP + photo-reduction measurements of the PsaL HIS strain show no effect on PSI activity in comparison to the WT trimeric PSI. Crystal structure of the PsaL HIS monomeric PSI reveals several alterations that occurred in the trimerisation site of PSI, primarily a deformation of the C-terminus of PsaL and loss of chlorophyll a and β-carotene molecules.

    • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Macromolecule Content 

  • Total Structure Weight: 349.06 kDa 
  • Atom Count: 23,566 
  • Modeled Residue Count: 2,233 
  • Deposited Residue Count: 2,233 
  • Unique protein chains: 11

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29254 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Go to UniProtKB:  P29254
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UniProt GroupP29254
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2731Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P29255 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P29255 
Go to UniProtKB:  P29255
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UniProt GroupP29255
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P32422 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II141Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for P19569 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV69Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12975 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III143Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P29256 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]40Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q55330 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]40Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q55329 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 2I [auth K]70Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P74564 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth L]137Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P37277 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth M]31Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P72986 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AA [auth A]
AC [auth B]
AD [auth B]
BA [auth A]
BC [auth B]
AA [auth A],
AC [auth B],
AD [auth B],
BA [auth A],
BC [auth B],
BD [auth B],
CA [auth A],
CC [auth B],
CD [auth B],
CE [auth J],
DA [auth A],
DC [auth B],
DE [auth J],
EA [auth A],
EC [auth B],
FA [auth A],
FC [auth B],
FE [auth K],
GA [auth A],
GC [auth B],
GE [auth K],
HA [auth A],
HC [auth B],
IA [auth A],
IB [auth A],
IC [auth B],
JA [auth A],
JC [auth B],
JE [auth L],
KA [auth A],
KB [auth A],
KC [auth B],
L [auth A],
LA [auth A],
LB [auth A],
LC [auth B],
M [auth A],
MA [auth A],
MB [auth B],
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],
PB [auth B],
PC [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
QD [auth B],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
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],
UD [auth F],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VD [auth F],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
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
SQD

Query on SQD


Download:Ideal Coordinates CCD File
OD [auth B],
TD [auth F]		1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG

Query on LMG


Download:Ideal Coordinates CCD File
KD [auth B],
MD [auth B]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
GB [auth A],
HB [auth A],
LD [auth B],
ND [auth B]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
C7Z

Query on C7Z


Download:Ideal Coordinates CCD File
BE [auth J],
XD [auth F]		(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
EQ3

Query on EQ3


Download:Ideal Coordinates CCD File
AE [auth I](3'R)-3'-hydroxy-beta,beta-caroten-4-one
C40 H54 O2
ZRCXVNZZDQGBQT-BANQPSJHSA-N
45D

Query on 45D


Download:Ideal Coordinates CCD File
NB [auth B]beta,beta-carotene-4,4'-dione
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N
ECH

Query on ECH


Download:Ideal Coordinates CCD File
GD [auth B],
KE [auth M]		beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
CB [auth A]
DB [auth A]
EB [auth A]
ED [auth B]
EE [auth J]
CB [auth A],
DB [auth A],
EB [auth A],
ED [auth B],
EE [auth J],
FB [auth A],
FD [auth B],
HD [auth B],
HE [auth K],
ID [auth B],
JB [auth A],
JD [auth B],
WD [auth F],
ZD [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT


Download:Ideal Coordinates CCD File
YD [auth F]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
AB [auth A],
DD [auth B]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
BB [auth A],
RD [auth C],
SD [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
IE [auth L],
PD [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
OB [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free:  0.295 (Depositor), 0.296 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.322α = 90
b = 178.658β = 90
c = 181.446γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilBelgium293579

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 2.0: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2025-10-01
    Changes: Advisory, Derived calculations