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- PDB-1fe1: CRYSTAL STRUCTURE PHOTOSYSTEM II -

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Basic information

Entry
Database: PDB / ID: 1fe1
TitleCRYSTAL STRUCTURE PHOTOSYSTEM II
Components(PROTEIN (PHOTOSYSTEM II: SUBUNIT ...) x 9
KeywordsPHOTOSYNTHESIS/ELECTRON TRANSPORT / PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / CORE- ANTEN A LIGHT-HARVESTING SYSTEM / THERMOPHILIC CYANOBACTERIUM / MEMBRANE PROTEIN / PHOTOSYNTHESIS-ELECTRON TRANSPORT COMPLEX
Function / homology: / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / : / PHEOPHYTIN A / Chem-PLA / TYROSINE
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.8 Å
AuthorsZouni, A. / Witt, H.-T. / Kern, J. / Fromme, P. / Krauss, N. / Saenger, W. / Orth, P.
CitationJournal: 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
DepositionJul 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_conn_type / 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: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBA)
B: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBD)
C: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBC)
D: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBB)
E: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBE)
F: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBF)
G: PROTEIN (PHOTOSYSTEM II: SUBUNIT UNKNOWN)
H: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBO)
I: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBV)
J: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBA)
K: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBD)
L: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBC)
M: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBB)
N: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBE)
O: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBF)
P: PROTEIN (PHOTOSYSTEM II: SUBUNIT UNKNOWN)
Q: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBO)
R: PROTEIN (PHOTOSYSTEM II: SUBUNIT PSBV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,435108
Polymers211,04418
Non-polymers65,39190
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.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein 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 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 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 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 PROTEIN (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 PROTEIN (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 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 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 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 , 8 types, 90 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-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO3
#12: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#13: Chemical
ChemComp-PHO / PHEOPHYTIN A


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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#15: Chemical ChemComp-PLA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID / N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE


Mass: 378.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N2O9P
#16: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


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

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Details

Has protein modificationN

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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: 293 K / Method: batch method / pH: 7
Details: POLYETHYLENGLYCOL 2000, HEPES-BUFFER, CACL2 , pH 7.00, BATCH METHOD, temperature 293K
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X1110.9
SYNCHROTRONEMBL/DESY, HAMBURG BW7B20.9
SYNCHROTRONELETTRA 5.2R30.9
SYNCHROTRONESRF ID240.9
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 1, 1999
MARRESEARCH2CCDJan 1, 1999
MARRESEARCH3IMAGE PLATEJan 1, 1999
MARRESEARCH4CCDJan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.8→20 Å / Num. all: 84964 / Num. obs: 84964 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / 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
Reflection
*PLUS
Highest resolution: 3.8 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 3.2 %
Reflection shell
*PLUS
% possible obs: 84.5 % / Mean I/σ(I) obs: 3.4

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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 ANGSTROEM USING 6 HEAVY ATOM DERIVATIVES. FOR DETAILS SEE ZOUNI ET AL. THE CADIMIUM DERIVATIVE HAS A RESOLUTION OF 3.8 ANGSTROEM. ...Details: THE STRUCTURE WAS SOLVED TO A RESOLUTION OF 4.2 ANGSTROEM USING 6 HEAVY ATOM DERIVATIVES. FOR DETAILS SEE ZOUNI ET AL. THE CADIMIUM DERIVATIVE HAS A RESOLUTION OF 3.8 ANGSTROEM. PHASEEXTENSION FROM 4.2 TILL 3.8 ANGSTROEM WAS PERFORMED USING TWO-FOLD NONCRYSTALLOGRAPHIC SYMMETRY AND SOLVENT FLATTENING.
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 1852 0 4328
Refinement
*PLUS
Rfactor obs: 0.59
Solvent computation
*PLUS
Displacement parameters
*PLUS

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