4IXR | pdb_00004ixr

RT fs X-ray diffraction of Photosystem II, first illuminated state

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.90 Å
  • R-Value Free: 
    0.313 (Depositor), 0.321 (DCC) 
  • R-Value Work: 
    0.285 (Depositor), 0.288 (DCC) 
  • R-Value Observed: 
    0.286 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 

Literature

Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

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

(2013) Science 340: 491-495

  • DOI: https://doi.org/10.1126/science.1234273
  • Primary Citation Related Structures: 
    4IXQ, 4IXR

  • PubMed Abstract: 

    Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.

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

Macromolecule Content 

  • Total Structure Weight: 765.69 kDa 
  • Atom Count: 50,232 
  • Modeled Residue Count: 5,270 
  • Deposited Residue Count: 5,706 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A,
U [auth a]		360Thermosynechococcus vestitusMutation(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 core light harvesting proteinB,
V [auth b]		510Thermosynechococcus vestitusMutation(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 proteinC,
W [auth c]		461Thermosynechococcus vestitusMutation(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,
X [auth d]		352Thermosynechococcus vestitusMutation(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,
Y [auth e]		84Thermosynechococcus vestitusMutation(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 f]		45Thermosynechococcus vestitusMutation(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 HAA [auth h],
G [auth H]		66Thermosynechococcus vestitusMutation(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 i],
H [auth I]		38Thermosynechococcus vestitusMutation(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 j],
I [auth J]		40Thermosynechococcus vestitusMutation(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 k],
J [auth K]		46Thermosynechococcus vestitusMutation(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 l],
K [auth L]		37Thermosynechococcus vestitusMutation(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 MFA [auth m],
L [auth M]		36Thermosynechococcus vestitusMutation(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 polypeptideGA [auth o],
M [auth O]		272Thermosynechococcus vestitusMutation(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 t],
N [auth T]		32Thermosynechococcus vestitusMutation(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 proteinIA [auth u],
O [auth U]		134Thermosynechococcus vestitusMutation(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 v],
P [auth V]		163Thermosynechococcus vestitusMutation(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 g],
Q [auth y]		46Thermosynechococcus vestitusMutation(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 proteinLA [auth x],
R [auth X]		41Thermosynechococcus vestitusMutation(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 ZMA [auth z],
S [auth Z]		62Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein YNA [auth Y],
T [auth G]		28Thermosynechococcus vestitusMutation(s): 0 

Small Molecules

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

Query on DGD


Download:Ideal Coordinates CCD File
AC [auth B]
AD [auth C]
BD [auth C]
GC [auth B]
MD [auth D]
AC [auth B],
AD [auth C],
BD [auth C],
GC [auth B],
MD [auth D],
MG [auth c],
NG [auth c],
OG [auth c],
QE [auth a],
SF [auth b],
XE [auth b],
YA [auth A],
YG [auth d],
ZC [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]
CF [auth b]
AF [auth b],
AG [auth c],
BF [auth b],
BG [auth c],
CF [auth b],
CG [auth c],
DF [auth b],
DG [auth c],
ED [auth D],
EF [auth b],
EG [auth c],
FF [auth b],
FG [auth c],
GB [auth B],
GD [auth D],
GF [auth b],
GG [auth c],
HB [auth B],
HE [auth a],
HF [auth b],
HG [auth c],
IB [auth B],
IE [auth a],
IF [auth b],
IG [auth c],
JB [auth B],
JC [auth C],
JE [auth a],
JF [auth b],
JG [auth c],
KB [auth B],
KC [auth C],
KF [auth b],
LB [auth B],
LC [auth C],
LF [auth b],
MB [auth B],
MC [auth C],
ME [auth a],
MF [auth b],
NB [auth B],
NC [auth C],
NF [auth b],
OB [auth B],
OC [auth C],
OF [auth b],
PB [auth B],
PC [auth C],
PF [auth b],
QA [auth A],
QB [auth B],
QC [auth C],
RA [auth A],
RB [auth B],
RC [auth C],
RG [auth d],
SA [auth A],
SB [auth B],
SC [auth C],
SG [auth d],
TB [auth B],
TC [auth C],
UA [auth A],
UB [auth B],
UC [auth C],
VB [auth B],
VC [auth C],
XF [auth c],
YF [auth c],
ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO


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FD [auth D],
KE [auth a],
LE [auth a],
TA [auth A]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD


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AB [auth A]
CH [auth f]
EB [auth A]
EE [auth a]
FC [auth B]
AB [auth A],
CH [auth f],
EB [auth A],
EE [auth a],
FC [auth B],
LD [auth D],
QD [auth F],
SE [auth a],
WE [auth b],
XG [auth d]
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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AH [auth e]
BB [auth A]
BC [auth B]
CC [auth B]
CD [auth C]
AH [auth e],
BB [auth A],
BC [auth B],
CC [auth B],
CD [auth C],
DD [auth C],
EH [auth i],
FB [auth A],
FE [auth a],
JD [auth D],
KD [auth D],
KH [auth k],
MH [auth m],
OD [auth E],
PG [auth c],
SD [auth I],
TE [auth a],
TF [auth b],
UF [auth b],
VG [auth d],
WG [auth d],
XD [auth M]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9


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GH [auth j]
HD [auth D]
NE [auth a]
TG [auth d]
UD [auth J]
GH [auth j],
HD [auth D],
NE [auth a],
TG [auth d],
UD [auth J],
VA [auth A]
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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CB [auth A],
RE [auth a],
UE [auth a],
ZA [auth A]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM


Download:Ideal Coordinates CCD File
BH [auth f],
CE [auth V],
OH [auth v],
PD [auth F]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR


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AE [auth T]
BE [auth T]
DE [auth y]
DH [auth h]
HH [auth j]
AE [auth T],
BE [auth T],
DE [auth y],
DH [auth h],
HH [auth j],
ID [auth D],
JH [auth k],
KG [auth c],
LG [auth c],
PE [auth a],
PH [auth z],
QF [auth b],
RD [auth H],
RF [auth b],
UG [auth d],
VD [auth J],
WB [auth B],
WC [auth C],
XA [auth A],
XB [auth B],
XC [auth C],
YB [auth B],
YC [auth C],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT


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DC [auth B]
EC [auth B]
FH [auth i]
HC [auth B]
IC [auth B]
DC [auth B],
EC [auth B],
FH [auth i],
HC [auth B],
IC [auth B],
LH [auth m],
ND [auth D],
TD [auth I],
VF [auth b],
WF [auth b],
YD [auth M],
YE [auth b],
ZE [auth b],
ZG [auth d]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEC

Query on OEC


Download:Ideal Coordinates CCD File
OE [auth a],
WA [auth A]		OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-UHFFFAOYSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
PA [auth A],
QG [auth d]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
GE [auth a],
OA [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
IH [auth k],
NH [auth o],
WD [auth K],
ZD [auth O]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
DB [auth A],
VE [auth a]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.90 Å
  • R-Value Free:  0.313 (Depositor), 0.321 (DCC) 
  • R-Value Work:  0.285 (Depositor), 0.288 (DCC) 
  • R-Value Observed: 0.286 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.976α = 90
b = 227.568β = 90
c = 306.994γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
cctbx.xfeldata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2013-05-08
    Changes: Database references
  • Version 2.0: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 2.1: 2024-10-16
    Changes: Data collection, Structure summary