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Basic information

Entry
Database: PDB / ID: 1ilx
TitleExcited State Dynamics in Photosystem II Revised. New Insights from the X-ray Structure.
Components(PHOTOSYSTEM II: SUBUNIT ...) x 9
KeywordsPHOTOSYNTHESIS / antenna chlorophyll / exitation transfer
Function / homology: / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / : / PHEOPHYTIN A / Chem-PL9
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.8 Å
AuthorsVasilev, S. / Orth, P. / Zouni, A. / Owens, T.G. / Bruce, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Excited-state dynamics in photosystem II: insights from the x-ray crystal structure.
Authors: Vasil'ev, S. / Orth, P. / Zouni, A. / Owens, T.G. / Bruce, D.
#1: Journal: Nature / Year: 2001
Title: CRYSTAL STRUCTURE OF PHOTOSYSTEM II FROM SYNECHOCOCCUS ELONGATUS AT 3.8 A RESOLUTION.
Authors: Zouni, A. / Witt, H.-T. / Kern, J. / Fromme, P. / Krauss, N. / Saenger, W. / Orth, P.
History
DepositionMay 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_validate_chiral / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOTOSYSTEM II: SUBUNIT PSBA
B: PHOTOSYSTEM II: SUBUNIT PSBD
C: PHOTOSYSTEM II: SUBUNIT PSBC
D: PHOTOSYSTEM II: SUBUNIT PSBB
E: PHOTOSYSTEM II: SUBUNIT PSBE
F: PHOTOSYSTEM II: SUBUNIT PSBF
G: PHOTOSYSTEM II: SUBUNIT UNKNOWN
H: PHOTOSYSTEM II: SUBUNIT PSBO
I: PHOTOSYSTEM II: SUBUNIT PSBV
J: PHOTOSYSTEM II: SUBUNIT PSBA
K: PHOTOSYSTEM II: SUBUNIT PSBD
L: PHOTOSYSTEM II: SUBUNIT PSBC
M: PHOTOSYSTEM II: SUBUNIT PSBB
N: PHOTOSYSTEM II: SUBUNIT PSBE
O: PHOTOSYSTEM II: SUBUNIT PSBF
P: PHOTOSYSTEM II: SUBUNIT UNKNOWN
Q: PHOTOSYSTEM II: SUBUNIT PSBO
R: PHOTOSYSTEM II: SUBUNIT PSBV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,813110
Polymers211,04418
Non-polymers70,76992
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.010, 226.720, 308.290
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

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PHOTOSYSTEM II: SUBUNIT ... , 9 types, 18 molecules AJBKCLDMENFOGPHQIR

#1: Protein PHOTOSYSTEM II: SUBUNIT PSBA / Coordinate model: Cα atoms only


Mass: 14400.733 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#2: Protein PHOTOSYSTEM II: SUBUNIT PSBD / Coordinate model: Cα atoms only


Mass: 14826.253 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#3: Protein PHOTOSYSTEM II: SUBUNIT PSBC / Coordinate model: Cα atoms only


Mass: 13294.380 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#4: Protein PHOTOSYSTEM II: SUBUNIT PSBB / Coordinate model: Cα atoms only


Mass: 13209.274 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#5: Protein/peptide PHOTOSYSTEM II: SUBUNIT PSBE / Coordinate model: Cα atoms only


Mass: 3422.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#6: Protein/peptide PHOTOSYSTEM II: SUBUNIT PSBF / Coordinate model: Cα atoms only


Mass: 2571.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#7: Protein PHOTOSYSTEM II: SUBUNIT UNKNOWN / Coordinate model: Cα atoms only


Mass: 26570.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#8: Protein PHOTOSYSTEM II: SUBUNIT PSBO / Coordinate model: Cα atoms only


Mass: 9805.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE, LUMEN
#9: Protein PHOTOSYSTEM II: SUBUNIT PSBV / Coordinate model: Cα atoms only


Mass: 7422.140 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE, LUMEN

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Non-polymers , 7 types, 92 molecules

#10: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#11: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#12: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#13: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#14: Chemical ChemComp-PL9 / 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 / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#15: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#16: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 50

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Sample preparation

CrystalDensity % sol: 45 %
Crystal growTemperature: 300 K / Method: evaporation, recrystallization / pH: 7
Details: POLYETHYLENGLYCOL 2000, HEPES-BUFFER, CACL2, pH 7.00, EVAPORATION, RECRYSTALLIZATION, temperature 300K
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X1111
SYNCHROTRONMPG/DESY, HAMBURG BW621
SYNCHROTRONELETTRA 5.2R31
SYNCHROTRONESRF ID241
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 1, 1999
MARRESEARCH2CCDJan 1, 1999
MARRESEARCH3IMAGE PLATEJan 1, 1999
MARRESEARCH4CCDJan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→20 Å / Num. obs: 84964 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 102 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.1
Reflection shellResolution: 3.8→3.91 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.418 / % possible all: 84.5

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Processing

Software
NameClassification
MLPHAREphasing
DMmodel building
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.8→20 Å
Details: THE STRUCTURE WAS SOLVED TO A RESOLUTION OF 4.2 ANGSTROM USING 6 HEAVY ATOM DERIVATIVES. FOR DETAILS SEE ZOUNI ET AL. THE CADIMIUM DERIVATIVE HAS A RESOLUTION OF 3.8 ANGSTROM. PHASEEXTENSION ...Details: THE STRUCTURE WAS SOLVED TO A RESOLUTION OF 4.2 ANGSTROM USING 6 HEAVY ATOM DERIVATIVES. FOR DETAILS SEE ZOUNI ET AL. THE CADIMIUM DERIVATIVE HAS A RESOLUTION OF 3.8 ANGSTROM. PHASEEXTENSION FROM 4.2 TILL 3.8 ANGSTROM WAS PERFORMED USING TWO-FOLD NONCRYSTALLOGRAPHIC SYMMETRY AND SOLVENT FLATTENING.
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 2118 0 4594

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