5MX2 | pdb_00005mx2

Photosystem II depleted of the Mn4CaO5 cluster at 2.55 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.260 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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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

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II.

Zhang, M.Bommer, M.Chatterjee, R.Hussein, R.Yano, J.Dau, H.Kern, J.Dobbek, H.Zouni, A.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.26933
  • Primary Citation Related Structures: 
    5MX2

  • PubMed Abstract: 

    In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn 4 CaO 5 -cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn 4 CaO 5 -cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn 4 CaO 5 -cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn 4 CaO 5 -cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.


  • Organizational Affiliation
    • Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 756.82 kDa 
  • Atom Count: 50,407 
  • Modeled Residue Count: 5,253 
  • Deposited Residue Count: 5,700 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
T [auth a]
344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]
510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]
461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]
352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]
84Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]
45Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]
66Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]
46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]
36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]
272Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]
32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]
134Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]
163Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12MA [auth y],
Q [auth Y]
46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinJA [auth x],
R [auth X]
41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth z],
S [auth Z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein YKA [auth R],
LA [auth r]
41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKM3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence

Small Molecules

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

Query on DGD



Download:Ideal Coordinates CCD File
JH [auth h]
LG [auth c]
MG [auth c]
NG [auth c]
SD [auth H]
JH [auth h],
LG [auth c],
MG [auth c],
NG [auth c],
SD [auth H],
UC [auth C],
VC [auth C],
WC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AF [auth b]
AG [auth c]
BF [auth b]
BG [auth c]
CB [auth B]
AF [auth b],
AG [auth c],
BF [auth b],
BG [auth c],
CB [auth B],
CD [auth D],
CF [auth b],
CG [auth c],
DB [auth B],
DD [auth D],
DF [auth b],
DG [auth c],
EB [auth B],
EF [auth b],
EG [auth c],
FB [auth B],
FC [auth C],
FF [auth b],
FG [auth c],
GB [auth B],
GC [auth C],
GF [auth b],
GG [auth c],
HB [auth B],
HC [auth C],
HE [auth a],
HF [auth b],
HG [auth c],
IB [auth B],
IC [auth C],
IE [auth a],
IF [auth b],
IG [auth c],
JB [auth B],
JC [auth C],
JF [auth b],
JG [auth c],
KB [auth B],
KC [auth C],
KE [auth a],
LB [auth B],
LC [auth C],
MB [auth B],
MC [auth C],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
PB [auth B],
PC [auth C],
QA [auth A],
QB [auth B],
QC [auth C],
QD [auth H],
RA [auth A],
RC [auth C],
TA [auth A],
UE [auth b],
UG [auth d],
VE [auth b],
VG [auth d],
WE [auth b],
WG [auth d],
XE [auth b],
XF [auth c],
YE [auth b],
YF [auth c],
ZA [auth A],
ZE [auth b],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
BD [auth D],
JE [auth a],
RE [auth a],
SA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



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HH [auth f]
LD [auth D]
NE [auth a]
PE [auth a]
SE [auth b]
HH [auth f],
LD [auth D],
NE [auth a],
PE [auth a],
SE [auth b],
WA [auth A],
XD [auth L],
YA [auth A]
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
EC [auth C]
GH [auth f]
JD [auth D]
OG [auth c]
PF [auth b]
EC [auth C],
GH [auth f],
JD [auth D],
OG [auth c],
PF [auth b],
RG [auth c],
RH [auth m],
UB [auth B],
WB [auth B],
WF [auth c],
XC [auth C],
ZC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
FD [auth D],
ME [auth a],
VA [auth A],
YG [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



Download:Ideal Coordinates CCD File
AH [auth d]
EH [auth e]
GD [auth D]
HD [auth D]
ID [auth D]
AH [auth d],
EH [auth e],
GD [auth D],
HD [auth D],
ID [auth D],
OD [auth E],
OH [auth l],
TF [auth b],
YD [auth L],
ZG [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC

Query on HEC



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DE [auth V],
UH [auth v]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
FH [auth e],
PD [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



Download:Ideal Coordinates CCD File
BE [auth T]
ED [auth D]
IH [auth h]
KF [auth b]
KG [auth c]
BE [auth T],
ED [auth D],
IH [auth h],
KF [auth b],
KG [auth c],
LE [auth a],
LF [auth b],
MF [auth b],
NH [auth k],
RB [auth B],
RD [auth H],
SB [auth B],
SC [auth C],
SG [auth c],
TB [auth B],
TC [auth C],
TG [auth c],
TH [auth t],
UA [auth A],
VD [auth K],
WD [auth K],
XG [auth d]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LFA

Query on LFA



Download:Ideal Coordinates CCD File
AB [auth A]
AC [auth B]
AE [auth M]
BC [auth B]
BH [auth d]
AB [auth A],
AC [auth B],
AE [auth M],
BC [auth B],
BH [auth d],
CC [auth B],
CE [auth T],
CH [auth d],
DC [auth B],
DH [auth d],
KD [auth D],
KH [auth i],
LH [auth i],
MD [auth D],
MH [auth j],
ND [auth D],
NF [auth b],
OE [auth a],
OF [auth b],
PG [auth c],
PH [auth m],
QF [auth b],
QG [auth c],
QH [auth m],
RF [auth b],
SF [auth b],
SH [auth t],
TD [auth I],
TE [auth b],
UD [auth J],
UF [auth b],
VB [auth B],
VF [auth b],
XA [auth A],
XB [auth B],
YB [auth B],
YC [auth C],
ZB [auth B],
ZD [auth M]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
AD [auth D],
QE [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE

Query on FE



Download:Ideal Coordinates CCD File
BB [auth A],
EE [auth a]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
FE [auth a],
GE [auth a],
OA [auth A],
PA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.260 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.326α = 90
b = 219.617β = 90
c = 304.043γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1078

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-09-25
    Changes: Data collection, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Derived calculations
  • Version 2.0: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 3.0: 2024-05-29
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 3.1: 2024-10-09
    Changes: Structure summary