Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.56 Å
  • R-Value Free: 
    0.385 (Depositor), 0.365 (DCC) 
  • R-Value Work: 
    0.366 (Depositor), 0.343 (DCC) 
  • R-Value Observed: 
    0.367 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.

Kern, J.Alonso-Mori, R.Hellmich, J.Tran, R.Hattne, J.Laksmono, H.Glockner, C.Echols, N.Sierra, R.G.Sellberg, J.Lassalle-Kaiser, B.Gildea, R.J.Glatzel, P.Grosse-Kunstleve, R.W.Latimer, M.J.McQueen, T.A.DiFiore, D.Fry, A.R.Messerschmidt, M.Miahnahri, A.Schafer, D.W.Seibert, M.M.Sokaras, D.Weng, T.C.Zwart, P.H.White, W.E.Adams, P.D.Bogan, M.J.Boutet, S.Williams, G.J.Messinger, J.Sauter, N.K.Zouni, A.Bergmann, U.Yano, J.Yachandra, V.K.

(2012) Proc Natl Acad Sci U S A 109: 9721-9726

  • DOI: https://doi.org/10.1073/pnas.1204598109
  • Primary Citation Related Structures: 
    4FBY

  • PubMed Abstract: 

    Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This light-driven, four-photon reaction is catalyzed by the Mn(4)CaO(5) cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (< 50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the "probe before destroy" approach using an X-ray free electron laser works even for the highly-sensitive Mn(4)CaO(5) cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn(4)CaO(5) cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.


  • Organizational Affiliation
    • Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 741.33 kDa 
  • Atom Count: 50,232 
  • Modeled Residue Count: 5,270 
  • Deposited Residue Count: 5,482 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A,
U [auth G]
344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB,
V [auth N]
510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC,
W [auth P]
461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth Q]
352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth R]
83Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth S]
44Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth W],
G [auth H]
65Thermosynechococcus 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 IBA [auth a],
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 JCA [auth b],
I [auth J]
39Thermosynechococcus 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 KDA [auth c],
J [auth K]
37Thermosynechococcus 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 LEA [auth d],
K [auth L]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth e],
L [auth M]
36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth f],
M [auth O]
246Thermosynechococcus 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 THA [auth g],
N [auth T]
32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth h],
O [auth U]
104Thermosynechococcus 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-550JA [auth i],
P [auth V]
137Thermosynechococcus 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 ycf12KA [auth m],
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 protein XLA [auth j],
R [auth X]
40Thermosynechococcus 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 YMA [auth k],
S [auth Y]
28Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZNA [auth l],
T [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

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
DC [auth B]
DH [auth W]
HG [auth P]
IG [auth P]
JD [auth D]
DC [auth B],
DH [auth W],
HG [auth P],
IG [auth P],
JD [auth D],
LE [auth G],
LG [auth P],
TC [auth C],
UA [auth A],
UE [auth N],
UG [auth Q],
VC [auth C],
WB [auth B],
XC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AF [auth N]
AG [auth P]
BF [auth N]
BG [auth P]
CB [auth B]
AF [auth N],
AG [auth P],
BF [auth N],
BG [auth P],
CB [auth B],
CD [auth D],
CF [auth N],
CG [auth P],
DB [auth B],
DF [auth N],
EB [auth B],
EF [auth N],
EG [auth P],
FB [auth B],
FD [auth D],
FE [auth G],
FF [auth N],
GB [auth B],
GC [auth C],
GE [auth G],
GF [auth N],
GG [auth P],
HB [auth B],
HC [auth C],
HF [auth N],
IB [auth B],
IC [auth C],
IE [auth G],
IF [auth N],
JB [auth B],
JC [auth C],
JF [auth N],
KB [auth B],
KC [auth C],
KE [auth G],
LB [auth B],
LC [auth C],
LF [auth N],
MB [auth B],
MC [auth C],
MF [auth N],
NB [auth B],
NC [auth C],
OA [auth A],
OB [auth B],
OC [auth C],
OF [auth N],
PA [auth A],
PB [auth B],
QA [auth A],
QB [auth B],
QC [auth C],
QG [auth Q],
RB [auth B],
SA [auth A],
SC [auth C],
SF [auth P],
SG [auth Q],
TF [auth P],
UC [auth C],
UF [auth P],
VF [auth P],
WC [auth C],
WF [auth P],
XE [auth N],
XF [auth P],
YE [auth N],
YF [auth P],
ZE [auth N],
ZF [auth P]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
AD [auth D],
HE [auth G],
NG [auth Q],
RA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
BB [auth A]
BH [auth S]
CC [auth B]
EE [auth G]
ME [auth G]
BB [auth A],
BH [auth S],
CC [auth B],
EE [auth G],
ME [auth G],
OD [auth F],
TE [auth N],
TG [auth Q],
WA [auth A],
ZB [auth B]
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
DD [auth D]
ED [auth D]
FH [auth a]
KG [auth P]
LD [auth D]
DD [auth D],
ED [auth D],
FH [auth a],
KG [auth P],
LD [auth D],
LH [auth e],
MG [auth P],
ND [auth E],
NF [auth N],
OE [auth G],
OG [auth Q],
QF [auth N],
RD [auth I],
RG [auth Q],
VG [auth Q],
WD [auth M],
XA [auth A],
XB [auth B],
YB [auth B],
YC [auth C],
ZC [auth C],
ZG [auth R]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
BD [auth D]
HH [auth b]
JE [auth G]
PG [auth Q]
TA [auth A]
BD [auth D],
HH [auth b],
JE [auth G],
PG [auth Q],
TA [auth A],
TD [auth J]
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
NE [auth G],
PE [auth G],
VA [auth A],
YA [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
CE [auth V],
MD [auth E],
NH [auth i],
YG [auth R]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AE [auth T]
AH [auth S]
BE [auth T]
CH [auth W]
DE [auth Z]
AE [auth T],
AH [auth S],
BE [auth T],
CH [auth W],
DE [auth Z],
DG [auth P],
EH [auth a],
FG [auth P],
GD [auth D],
IH [auth b],
JG [auth P],
JH [auth c],
KF [auth N],
PC [auth C],
PD [auth H],
QD [auth I],
RC [auth C],
SB [auth B],
TB [auth B],
UB [auth B],
UD [auth J],
VB [auth B],
VD [auth K],
ZD [auth T]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
AC [auth B]
BC [auth B]
EC [auth B]
FC [auth B]
GH [auth a]
AC [auth B],
BC [auth B],
EC [auth B],
FC [auth B],
GH [auth a],
KD [auth D],
KH [auth e],
PF [auth N],
RF [auth N],
SD [auth I],
VE [auth N],
WE [auth N],
WG [auth Q],
XD [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEC

Query on OEC



Download:Ideal Coordinates CCD File
QE [auth G],
ZA [auth A]
OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
HD [auth D],
XG [auth Q]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
AB [auth A],
RE [auth G]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
MH [auth f],
YD [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
ID [auth D],
SE [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.56 Å
  • R-Value Free:  0.385 (Depositor), 0.365 (DCC) 
  • R-Value Work:  0.366 (Depositor), 0.343 (DCC) 
  • R-Value Observed: 0.367 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.783α = 90
b = 227.764β = 90
c = 308.63γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Non-polymer description
  • Version 1.2: 2013-01-09
    Changes: Database references
  • Version 1.3: 2016-12-21
    Changes: Data collection
  • Version 1.4: 2017-11-15
    Changes: Data collection
  • Version 1.5: 2017-11-29
    Changes: Database references
  • Version 1.6: 2018-02-14
    Changes: Data collection
  • Version 2.0: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 2.1: 2024-11-20
    Changes: Data collection, Structure summary