9I4T | pdb_00009i4t

Photosystem II from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Photosystem II from Arabidopsis thaliana

Forsman, J.A.Graca, A.T.Hussein, R.Hall, M.Messinger, J.Schroder, W.P.Aydin, A.O.

To be published.

Macromolecule Content 

  • Total Structure Weight: 1,288.9 kDa 
  • Atom Count: 76,824 
  • Modeled Residue Count: 7,548 
  • Deposited Residue Count: 9,452 
  • Unique protein chains: 24

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
Z [auth a]
353Arabidopsis thalianaMutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P83755 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinAA [auth b],
B
508Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56777 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinBA [auth c],
C
473Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56778 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinCA [auth d],
D
353Arabidopsis thalianaMutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P56761 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaDA [auth e],
E
83Arabidopsis thalianaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaEA [auth f],
F
39Arabidopsis thalianaMutation(s): 1 
UniProt
Find proteins for P62095 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 1, chloroplasticFA [auth g],
G,
MA [auth n],
N
267Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P04778 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HGA [auth h],
H
73Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56780 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IHA [auth i],
I
36Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P62100 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JIA [auth j],
J
40Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56781 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJA [auth k],
K
61Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56782 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LKA [auth l],
L
38Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P60129 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MLA [auth m],
M
34Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P62109 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1-1, chloroplasticNA [auth o],
O
332Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P23321 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 2-1, chloroplasticOA [auth p],
P
263Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q42029 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 3-1, chloroplasticPA [auth q],
Q
224Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9XFT3 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP29.1, chloroplasticQA [auth r],
R
290Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q07473 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP26, chloroplasticRA [auth s],
S
280Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9XF89 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TSA [auth t],
T
33Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P61839 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 5 kDa protein, chloroplasticTA [auth u],
U
103Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q39195 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplasticUA [auth w],
V [auth W]
133Arabidopsis thalianaMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Expressed proteinVA [auth x],
W [auth X]
116Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SKI3 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2.1, chloroplasticWA [auth y],
X [auth Y]
265Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SHR7 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZXA [auth z],
Y [auth Z]
62Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56790 (Arabidopsis thaliana)
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Reference Sequence

Small Molecules

Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
CC [auth B]
HJ [auth c]
HN [auth y]
JJ [auth c]
NC [auth C]
CC [auth B],
HJ [auth c],
HN [auth y],
JJ [auth c],
NC [auth C],
OC [auth C],
OI [auth b],
RC [auth C],
RI [auth c],
SG [auth Y]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



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AF [auth N]
AL [auth n]
BF [auth N]
BL [auth n]
BN [auth y]
AF [auth N],
AL [auth n],
BF [auth N],
BL [auth n],
BN [auth y],
CL [auth n],
CN [auth y],
DH [auth Y],
DK [auth g],
DM [auth r],
EE [auth G],
EF [auth R],
EN [auth y],
FL [auth n],
FM [auth r],
GH [auth Y],
HG [auth S],
HH [auth Y],
HK [auth g],
IG [auth S],
IK [auth g],
IM [auth s],
JK [auth g],
KK [auth g],
LG [auth S],
LN [auth y],
ML [auth n],
ND [auth G],
NE [auth N],
NL [auth n],
NN [auth y],
OE [auth N],
OL [auth r],
PD [auth G],
PF [auth R],
PK [auth g],
RD [auth G],
RG [auth Y],
SF [auth R],
SM [auth s],
UE [auth N],
VD [auth G],
VE [auth N],
VF [auth R],
VM [auth s],
WG [auth Y],
WL [auth r],
WM [auth s],
XD [auth G],
XF [auth S]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



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AB [auth A]
AC [auth B]
AD [auth D]
AE [auth G]
AH [auth Y]
AB [auth A],
AC [auth B],
AD [auth D],
AE [auth G],
AH [auth Y],
AI [auth b],
AJ [auth c],
AK [auth g],
AM [auth r],
BH [auth Y],
BI [auth b],
BK [auth g],
BM [auth r],
CB [auth A],
CF [auth N],
CG [auth S],
CH [auth Y],
CI [auth b],
CM [auth r],
DE [auth G],
DF [auth N],
DG [auth S],
DI [auth b],
DJ [auth c],
DL [auth n],
DN [auth y],
EG [auth S],
EI [auth b],
EJ [auth c],
EK [auth g],
EL [auth n],
EM [auth r],
FD [auth D],
FE [auth G],
FF [auth R],
FG [auth S],
FH [auth Y],
FI [auth b],
FJ [auth c],
FN [auth y],
GG [auth S],
GI [auth b],
GJ [auth c],
GL [auth n],
GM [auth s],
HI [auth b],
IC [auth C],
ID [auth D],
II [auth b],
IJ [auth c],
IN [auth y],
JB [auth B],
JC [auth C],
JF [auth R],
JG [auth S],
JH [auth a],
JL [auth n],
JM [auth s],
JN [auth y],
KB [auth B],
KC [auth C],
KF [auth R],
KG [auth S],
KI [auth b],
KJ [auth c],
KM [auth s],
LB [auth B],
LC [auth C],
LD [auth D],
LF [auth R],
LI [auth b],
LK [auth g],
LM [auth s],
MB [auth B],
MC [auth C],
MF [auth R],
MI [auth b],
MM [auth s],
MN [auth y],
NB [auth B],
NF [auth R],
NJ [auth d],
NK [auth g],
OB [auth B],
OD [auth G],
OJ [auth d],
OK [auth g],
ON [auth y],
PB [auth B],
PC [auth C],
PM [auth s],
PN [auth y],
QC [auth C],
QD [auth G],
QE [auth N],
QF [auth R],
QG [auth Y],
QH [auth a],
QL [auth r],
QM [auth s],
QN [auth y],
RB [auth B],
RE [auth N],
RF [auth R],
SB [auth B],
SD [auth G],
SE [auth N],
SH [auth a],
SI [auth c],
SL [auth r],
TB [auth B],
TC [auth C],
TD [auth G],
TE [auth N],
TF [auth R],
TI [auth c],
TL [auth r],
TM [auth s],
UB [auth B],
UC [auth C],
UF [auth R],
UG [auth Y],
UI [auth c],
UM [auth s],
VB [auth B],
VC [auth C],
VH [auth b],
VI [auth c],
VJ [auth d],
VL [auth r],
WE [auth N],
WH [auth b],
WI [auth c],
WK [auth n],
XB [auth B],
XC [auth C],
XE [auth N],
XG [auth Y],
XK [auth n],
XL [auth r],
YB [auth B],
YC [auth C],
YF [auth S],
YH [auth b],
YI [auth c],
YJ [auth g],
YK [auth n],
YL [auth r],
ZB [auth B],
ZC [auth C],
ZD [auth G],
ZF [auth S],
ZG [auth Y],
ZH [auth b],
ZJ [auth g],
ZK [auth n]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



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BB [auth A],
CD [auth D],
RH [auth a],
RJ [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
(Subject of Investigation/LOI)

Query on SQD



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DC [auth B]
EB [auth A]
HB [auth A]
KH [auth a]
PG [auth W]
DC [auth B],
EB [auth A],
HB [auth A],
KH [auth a],
PG [auth W],
PI [auth b],
UH [auth a],
ZM [auth w]
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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CJ [auth c]
DD [auth D]
EC [auth B]
HC [auth C]
OG [auth W]
CJ [auth c],
DD [auth D],
EC [auth B],
HC [auth C],
OG [auth W],
PJ [auth d],
QI [auth b],
WC [auth C],
YM [auth w],
ZI [auth c]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



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FB [auth A],
KD [auth D],
OH [auth a],
SJ [auth d]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG

Query on LHG



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AN [auth y]
GD [auth D]
GF [auth R]
HD [auth D]
JD [auth D]
AN [auth y],
GD [auth D],
GF [auth R],
HD [auth D],
JD [auth D],
KE [auth L],
LE [auth N],
MG [auth S],
MJ [auth d],
OM [auth s],
TJ [auth d],
UJ [auth d],
UK [auth l],
VG [auth Y],
VK [auth n],
XJ [auth g],
YD [auth G],
ZL [auth r]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM



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MD [auth E],
WJ [auth e]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NEX

Query on NEX



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AG [auth S]
BE [auth G]
CK [auth g]
GN [auth y]
HL [auth n]
AG [auth S],
BE [auth G],
CK [auth g],
GN [auth y],
HL [auth n],
HM [auth s],
IF [auth R],
ME [auth N],
PL [auth r],
TG [auth Y]
(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
XAT

Query on XAT



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FK [auth g]
GE [auth G]
HF [auth R]
KL [auth n]
QK [auth g]
FK [auth g],
GE [auth G],
HF [auth R],
KL [auth n],
QK [auth g],
RL [auth r],
WD [auth G],
ZE [auth N]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT

Query on LUT



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BG [auth S]
CE [auth G]
EH [auth Y]
GK [auth g]
IL [auth n]
BG [auth S],
CE [auth G],
EH [auth Y],
GK [auth g],
IL [auth n],
KN [auth y],
LL [auth n],
MK [auth g],
NM [auth s],
OF [auth R],
PE [auth N],
RM [auth s],
RN [auth y],
UD [auth G],
UL [auth r],
WF [auth S],
YE [auth N],
YG [auth Y]
(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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BC [auth B]
BJ [auth c]
DB [auth A]
ED [auth D]
GC [auth C]
BC [auth B],
BJ [auth c],
DB [auth A],
ED [auth D],
GC [auth C],
HE [auth H],
IE [auth J],
JE [auth K],
JI [auth b],
LH [auth a],
LJ [auth d],
NG [auth T],
NI [auth b],
QB [auth B],
RK [auth h],
SC [auth C],
SK [auth j],
TK [auth k],
WB [auth B],
XH [auth b],
XI [auth c],
XM [auth t]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



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BD [auth D],
QJ [auth d]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
(Subject of Investigation/LOI)

Query on OEX



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FC [auth C],
PH [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT

Query on BCT



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IB [auth A],
MH [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
(Subject of Investigation/LOI)

Query on FE2



Download:Ideal Coordinates CCD File
GB [auth A],
TH [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
IH [auth a],
NH [auth a],
YA [auth A],
ZA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sven och Lilly Lawskis fond for naturvetenskaplig forskningSweden--
Swedish Research CouncilSweden2020-03809
Carl Trygger FoundationSwedenCTS 19.324
Kempe FoundationSwedenJCK-2030
German Research Foundation (DFG)GermanyTP A5

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release