5OY0 | pdb_00005oy0

Structure of synechocystis photosystem I trimer at 2.5A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.264 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history

Literature

Structure and function of wild-type and subunit-depleted photosystem I in Synechocystis.

Malavath, T.Caspy, I.Netzer-El, S.Y.Klaiman, D.Nelson, N.

(2018) Biochim Biophys Acta 1859: 645-654

  • DOI: https://doi.org/10.1016/j.bbabio.2018.02.002
  • Primary Citation Related Structures: 
    5OY0

  • PubMed Abstract: 

    The ability of photosynthetic organisms to use the sun's light as a sole source of energy sustains life on our planet. Photosystems I (PSI) and II (PSII) are large, multi-subunit, pigment-protein complexes that enable photosynthesis, but this intriguing process remains to be explained fully. Currently, crystal structures of these complexes are available for thermophilic prokaryotic cyanobacteria. The mega-Dalton trimeric PSI complex from thermophilic cyanobacterium, Thermosynechococcus elongatus, was solved at 2.5 Å resolution with X-ray crystallography. That structure revealed the positions of 12 protein subunits (PsaA-F, PsaI-M, and PsaX) and 127 cofactors. Although mesophilic organisms perform most of the world's photosynthesis, no well-resolved trimeric structure of a mesophilic organism exists. Our research model for a mesophilic cyanobacterium was Synechocystis sp. PCC6803. This study aimed to obtain well-resolved crystal structures of [1] a monomeric PSI with all subunits, [2] a trimeric PSI with a reduced number of subunits, and [3] the full, trimeric wild-type PSI complex. We only partially succeeded with the first two structures, but we successfully produced the trimeric PSI structure at 2.5 Å resolution. This structure was comparable to that of the thermophilic species, but we provided more detail. The PSI trimeric supercomplex consisted of 33 protein subunits, 72 carotenoids, 285 chlorophyll a molecules, 51 lipids, 9 iron-sulfur clusters, 6 plastoquinones, 6 putative calcium ions, and over 870 water molecules. This study showed that the structure of the PSI in Synechocystis sp. PCC6803 differed from previously described PSI structures. These findings have broadened our understanding of PSI structure.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

Macromolecule Content 

  • Total Structure Weight: 1,087.72 kDa 
  • Atom Count: 77,117 
  • Modeled Residue Count: 6,771 
  • Deposited Residue Count: 6,771 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
L [auth a]
751Synechocystis sp. PCC 6803Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
X [auth 2]
731Synechocystis sp. PCC 6803Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC,
Y [auth 3]
80Synechocystis sp. PCC 6803Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID,
O [auth d]
141Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVAA [auth 5],
E
69Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIBA [auth 6],
F,
Q [auth f]
143Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I],
R [auth i]
40Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXDA [auth 7],
H [auth J],
S [auth j]
40Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 2I [auth K]80Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth L],
U [auth l]
157Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIGA [auth 9],
K [auth M],
V [auth m]
31Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2M [auth b]729Synechocystis sp. PCC 6803Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerN [auth c]81Synechocystis sp. PCC 6803Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVP [auth e]68Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 2T [auth k]78Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1W [auth 1]744Synechocystis sp. PCC 6803Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIZ [auth 4]140Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIICA [auth h]38Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK 2EA [auth 8]79Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIFA [auth 0]154Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence

Small Molecules

Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
ZF [auth L]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AB [auth A]
AD [auth B]
AE [auth B]
AH [auth a]
AJ [auth b]
AB [auth A],
AD [auth B],
AE [auth B],
AH [auth a],
AJ [auth b],
AK [auth b],
AM [auth 1],
AN [auth 1],
AO [auth 1],
AP [auth 2],
AR [auth 0],
BB [auth A],
BD [auth B],
BE [auth B],
BH [auth a],
BJ [auth b],
BK [auth b],
BM [auth 1],
BN [auth 1],
BP [auth 2],
BR [auth 0],
CB [auth A],
CD [auth B],
CE [auth B],
CH [auth a],
CJ [auth b],
CK [auth b],
CM [auth 1],
CN [auth 1],
CO [auth 1],
CP [auth 2],
DB [auth A],
DD [auth B],
DE [auth B],
DF [auth F],
DH [auth a],
DJ [auth b],
DM [auth 1],
DN [auth 1],
DO [auth 2],
DP [auth 2],
EB [auth A],
ED [auth B],
EE [auth B],
EF [auth F],
EH [auth a],
EJ [auth b],
EL [auth j],
EM [auth 1],
EN [auth 1],
EO [auth 2],
EP [auth 2],
FB [auth A],
FD [auth B],
FE [auth B],
FG [auth a],
FH [auth a],
FJ [auth b],
FL [auth j],
FM [auth 1],
FN [auth 1],
FP [auth 2],
GB [auth A],
GD [auth B],
GE [auth B],
GG [auth a],
GH [auth a],
GI [auth a],
GJ [auth b],
GL [auth k],
GM [auth 1],
GN [auth 1],
GP [auth 2],
GQ [auth 2],
HA [auth A],
HB [auth A],
HD [auth B],
HG [auth a],
HH [auth a],
HI [auth a],
HJ [auth b],
HL [auth k],
HM [auth 1],
HN [auth 1],
HO [auth 2],
HP [auth 2],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth B],
IG [auth a],
IH [auth a],
II [auth a],
IJ [auth b],
IM [auth 1],
IN [auth 1],
IO [auth 2],
IP [auth 2],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth B],
JG [auth a],
JH [auth a],
JJ [auth b],
JM [auth 1],
JN [auth 1],
JO [auth 2],
JP [auth 2],
JQ [auth 6],
KA [auth A],
KB [auth A],
KD [auth B],
KG [auth a],
KH [auth a],
KI [auth a],
KJ [auth b],
KL [auth l],
KM [auth 1],
KN [auth 1],
KO [auth 2],
KP [auth 2],
KQ [auth 6],
LA [auth A],
LB [auth A],
LD [auth B],
LF [auth J],
LG [auth a],
LH [auth a],
LJ [auth b],
LL [auth l],
LM [auth 1],
LO [auth 2],
LP [auth 2],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth B],
MF [auth J],
MG [auth a],
MH [auth a],
MI [auth a],
MJ [auth b],
ML [auth l],
MM [auth 1],
MO [auth 2],
MP [auth 2],
NA [auth A],
NB [auth A],
ND [auth B],
NG [auth a],
NH [auth a],
NI [auth b],
NJ [auth b],
NM [auth 1],
NO [auth 2],
NP [auth 2],
OA [auth A],
OB [auth A],
OD [auth B],
OF [auth K],
OG [auth a],
OH [auth a],
OI [auth b],
OJ [auth b],
OM [auth 1],
OO [auth 2],
OP [auth 2],
PA [auth A],
PB [auth A],
PD [auth B],
PF [auth K],
PG [auth a],
PH [auth a],
PJ [auth b],
PM [auth 1],
PO [auth 2],
PP [auth 2],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth B],
QG [auth a],
QH [auth a],
QJ [auth b],
QM [auth 1],
QO [auth 2],
QP [auth 2],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RG [auth a],
RH [auth a],
RI [auth b],
RJ [auth b],
RM [auth 1],
RO [auth 2],
RP [auth 2],
RQ [auth 7],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SG [auth a],
SI [auth b],
SJ [auth b],
SK [auth b],
SM [auth 1],
SO [auth 2],
SP [auth 2],
SQ [auth 7],
TA [auth A],
TB [auth A],
TD [auth B],
TF [auth L],
TG [auth a],
TI [auth b],
TJ [auth b],
TK [auth b],
TM [auth 1],
TO [auth 2],
TP [auth 2],
TQ [auth 8],
UA [auth A],
UB [auth A],
UD [auth B],
UF [auth L],
UG [auth a],
UI [auth b],
UJ [auth b],
UM [auth 1],
UO [auth 2],
UQ [auth 8],
VA [auth A],
VC [auth B],
VD [auth B],
VF [auth L],
VG [auth a],
VI [auth b],
VJ [auth b],
VM [auth 1],
VO [auth 2],
WA [auth A],
WC [auth B],
WD [auth B],
WG [auth a],
WI [auth b],
WJ [auth b],
WK [auth f],
WM [auth 1],
WO [auth 2],
XA [auth A],
XC [auth B],
XD [auth B],
XE [auth B],
XG [auth a],
XI [auth b],
XJ [auth b],
XK [auth f],
XL [auth 1],
XM [auth 1],
XO [auth 2],
YA [auth A],
YC [auth B],
YD [auth B],
YE [auth B],
YG [auth a],
YI [auth b],
YJ [auth b],
YL [auth 1],
YM [auth 1],
YN [auth 1],
YO [auth 2],
ZA [auth A],
ZC [auth B],
ZD [auth B],
ZG [auth a],
ZI [auth b],
ZJ [auth b],
ZL [auth 1],
ZM [auth 1],
ZN [auth 1],
ZO [auth 2],
ZQ [auth 0]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD

Query on SQD



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CG [auth L]
FR [auth 0]
GF [auth F]
NK [auth b]
SE [auth B]
CG [auth L],
FR [auth 0],
GF [auth F],
NK [auth b],
SE [auth B],
YF [auth L],
ZK [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



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BI [auth a]
BQ [auth 2]
DI [auth a]
DQ [auth 2]
EC [auth A]
BI [auth a],
BQ [auth 2],
DI [auth a],
DQ [auth 2],
EC [auth A],
ER [auth 0],
GC [auth A],
KK [auth b],
LC [auth A],
MK [auth b],
OE [auth B],
OK [auth b],
QE [auth B],
RF [auth K],
UN [auth 1],
WN [auth 1]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
AG [auth L]
AI [auth a]
CF [auth F]
CI [auth a]
CQ [auth 2]
AG [auth L],
AI [auth a],
CF [auth F],
CI [auth a],
CQ [auth 2],
DC [auth A],
EG [auth M],
EI [auth a],
FC [auth A],
LI [auth a],
LK [auth b],
MQ [auth 6],
NC [auth A],
OC [auth A],
PC [auth A],
PE [auth B],
PL [auth l],
QL [auth l],
RE [auth B],
RL [auth l],
TL [auth l],
TN [auth 1],
VL [auth 1],
VN [auth 1],
WL [auth 1],
WQ [auth 0],
XQ [auth 0]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
ZEX

Query on ZEX



Download:Ideal Coordinates CCD File
DL [auth j],
FF [auth F],
KF [auth J],
QQ [auth 7]
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
C40 H56 O2
YRMDXLDAZBQLBK-WIHRHFSMSA-N
EQ3

Query on EQ3



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

Query on ECH



Download:Ideal Coordinates CCD File
BL [auth i]
DG [auth M]
GK [auth b]
KE [auth B]
PI [auth b]
BL [auth i],
DG [auth M],
GK [auth b],
KE [auth B],
PI [auth b],
UL [auth m],
XP [auth 2]
beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AC [auth A]
AL [auth i]
AQ [auth 2]
BC [auth A]
BO [auth 1]
AC [auth A],
AL [auth i],
AQ [auth 2],
BC [auth A],
BO [auth 1],
CC [auth A],
CL [auth j],
CR [auth 0],
DR [auth 0],
EK [auth b],
FK [auth b],
FO [auth 2],
FQ [auth 2],
HK [auth b],
HR [auth 9],
IE [auth B],
IF [auth I],
IK [auth b],
IL [auth k],
JE [auth B],
JI [auth a],
JK [auth b],
KC [auth A],
LE [auth B],
LQ [auth 6],
ME [auth B],
NE [auth B],
NF [auth J],
NL [auth l],
NN [auth 1],
OL [auth l],
ON [auth 1],
OQ [auth h],
PN [auth 1],
PQ [auth 7],
QF [auth K],
QN [auth 1],
RK [auth b],
RN [auth 1],
SN [auth 1],
UH [auth a],
VH [auth a],
VP [auth 2],
VQ [auth 8],
WE [auth B],
WF [auth L],
WH [auth a],
WP [auth 2],
XB [auth A],
XF [auth L],
XH [auth a],
YB [auth A],
YH [auth a],
YK [auth f],
YP [auth 2],
ZB [auth A],
ZH [auth a],
ZP [auth 2]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BG [auth L],
GR [auth 0],
HF [auth F],
SL [auth l],
XN [auth 1]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
DK [auth b]
HE [auth B]
LN [auth 1]
SH [auth a]
UP [auth 2]
DK [auth b],
HE [auth B],
LN [auth 1],
SH [auth a],
UP [auth 2],
VB [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AF [auth C]
BF [auth C]
HQ [auth 3]
IQ [auth 3]
MN [auth 1]
AF [auth C],
BF [auth C],
HQ [auth 3],
IQ [auth 3],
MN [auth 1],
TH [auth a],
UK [auth c],
VK [auth c],
WB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
FI [auth a],
HC [auth A],
VE [auth B],
ZE [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
EQ [auth 2]
JL [auth l]
PK [auth b]
SF [auth L]
TE [auth B]
EQ [auth 2],
JL [auth l],
PK [auth b],
SF [auth L],
TE [auth B],
YQ [auth 0]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
GO [auth 2],
QI [auth b],
UC [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
QK [auth b],
UE [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.264 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.17α = 90
b = 137.622β = 116.74
c = 225.095γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata reduction
XSCALEdata scaling
MOLREPphasing
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium293579
ISFIsrael71/14

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 2.0: 2019-10-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 2.1: 2019-11-20
    Changes: Advisory, Derived calculations
  • Version 3.0: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary