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- PDB-1c51: PHOTOSYNTHETIC REACTION CENTER AND CORE ANTENNA SYSTEM (TRIMERIC)... -

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Basic information

Entry
Database: PDB / ID: 1c51
TitlePHOTOSYNTHETIC REACTION CENTER AND CORE ANTENNA SYSTEM (TRIMERIC), ALPHA CARBON ONLY
Components(PROTEIN (PHOTOSYSTEM I: SUBUNIT ...) x 8
KeywordsPHOTOSYNTHESIS/ELECTRON TRANSPORT / PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / OXYGENIC PHOTOSYNTHESIS / CORE- ANTENNA LIGHT-HARVESTING SYSTEM / THERMOPHILIC CYANOBACTERIUM / HELIX-BUNDLE MEMBRANE PROTEIN / PHOTOSYNTHESIS-ELECTRON TRANSPORT COMPLEX
Function / homologyCHLOROPHYLL A / PHYLLOQUINONE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4 Å
AuthorsKlukas, O. / Schubert, W.D. / Jordan, P. / Krauss, N. / Fromme, P. / Witt, H.T. / Saenger, W.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Photosystem I, an improved model of the stromal subunits PsaC, PsaD, and PsaE.
Authors: Klukas, O. / Schubert, W.D. / Jordan, P. / Krauss, N. / Fromme, P. / Witt, H.T. / Saenger, W.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Localisation of Two Phylloquinones, Qk and Qk', in an Improved Electron Density Map of Photosystem I at 4-A Resolution
Authors: Klukas, O. / Schubert, W.-D. / Jordan, P. / Krauss, N. / Fromme, P. / Witt, H.T. / Saenger, W.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: Photosystem I of Synechococcus Elongatus at 4 A Resolution: Comprehensive Structure Analysis
Authors: Schubert, W.-D. / Klukas, O. / Krauss, N. / Saenger, W. / Fromme, P. / Witt, H.T.
#3: Journal: Nat.Struct.Biol. / Year: 1996
Title: Photosystem I at 4 A Resolution Represents the First Structural Model of a Joint Photosynthetic Reaction Centre and Core Antenna System
Authors: Krauss, N. / Schubert, W.-D. / Klukas, O. / Fromme, P. / Witt, H.T. / Saenger, W.
#4: Journal: Nature / Year: 1993
Title: Three-Dimensional Structure of System I of Photosynthesis at 6A Resolution
Authors: Krauss, N. / Hinrichs, W. / Witt, I. / Fromme, P. / Pritzkow, W. / Dauter, Z. / Betzel, C. / Wilson, K.S. / Witt, H.T. / Saenger, W.
#5: Journal: Ber.Bunsenges.Phys.Chem. / Year: 1988
Title: X-Ray Characterization of Single Crystals of the Reaction Center I of Water Splitting Photosynthesis
Authors: Witt, I. / Witt, H.T. / Di Fiore, D. / Rogner, M. / Hinrichs, W. / Saenger, W. / Granzin, J. / Betzel, C. / Dauter, Z.
History
DepositionOct 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 27, 2023Group: 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 / 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 / _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 I: SUBUNIT PSAA)
B: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAB )
C: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAC)
D: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAD)
E: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAE)
F: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAF)
K: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAK)
L: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,36585
Polymers157,0788
Non-polymers66,28877
Water00
1
A: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAA)
B: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAB )
C: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAC)
D: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAD)
E: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAE)
F: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAF)
K: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAK)
L: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAL)
hetero molecules

A: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAA)
B: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAB )
C: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAC)
D: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAD)
E: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAE)
F: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAF)
K: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAK)
L: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAL)
hetero molecules

A: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAA)
B: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAB )
C: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAC)
D: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAD)
E: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAE)
F: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAF)
K: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAK)
L: PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)670,096255
Polymers471,23324
Non-polymers198,863231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)286.000, 286.000, 167.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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PROTEIN (PHOTOSYSTEM I: SUBUNIT ... , 8 types, 8 molecules ABCDEFKL

#1: Protein PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAA) / Coordinate model: Cα atoms only


Mass: 50825.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#2: Protein PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAB ) / Coordinate model: Cα atoms only


Mass: 52698.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#3: Protein PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAC) / Coordinate model: Cα atoms only


Mass: 6571.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#4: Protein PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAD) / Coordinate model: Cα atoms only


Mass: 10656.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#5: Protein PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAE) / Coordinate model: Cα atoms only


Mass: 6400.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#6: Protein PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAF) / Coordinate model: Cα atoms only


Mass: 13039.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#7: Protein PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAK) / Coordinate model: Cα atoms only


Mass: 6656.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE
#8: Protein PROTEIN (PHOTOSYSTEM I: SUBUNIT PSAL) / Coordinate model: Cα atoms only


Mass: 10230.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE

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Non-polymers , 3 types, 77 molecules

#9: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#10: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Compound detailsCHAIN A COMPRISES ONE OF THE TWO LARGE, CENTRAL, MEMBRANE INTEGRAL SUBUNITS OF THE REACTION CENTER ...CHAIN A COMPRISES ONE OF THE TWO LARGE, CENTRAL, MEMBRANE INTEGRAL SUBUNITS OF THE REACTION CENTER OF PSI - EITHER PSAA OR PSAB. CHAIN B COMPRISES THE SECOND OF THE TWO LARGE, CENTRAL, MEMBRANE INTEGRAL SUBUNITS OF THE REACTION CENTER OF PSI - EITHER PSAB OR PSAA. CHAIN C COMPRISES THE MODEL OF THE STROMAL EXTRINSIC SUBUNIT OF PSI - PSAC. CHAIN F COMPRISES THOSE SECTIONS OF THE PRESENT MODEL LOCATED DISTAL TO THE TRIMERIZATION DOMAIN - PRESUMABLY SUBUNITS PSAF, PSAJ AND PSAM. CHAIN L COMPRISES THOSE SECTIONS OF THE PRESENT STRUCTURE MODEL IN CLOSE PROXIMITY TO THE TRIMERIZATION DOMAIN - PROBABLY SUBUNITS PSAI AND PSAL. CHAIN K COMPRISES SUBUNIT PSAK.
Nonpolymer detailsTHE ATOM NAMING OF THE CHLOROPHYLL MOLECULES IS ARBITRARY IN THE SENSE THAT THE AUTHORS DO NOT WISH ...THE ATOM NAMING OF THE CHLOROPHYLL MOLECULES IS ARBITRARY IN THE SENSE THAT THE AUTHORS DO NOT WISH TO IMPLY WHICH PYRROLE RING IS ADJACENT TO THE EXTRACYCLIC RING FIVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 5.8 Å3/Da / Density % sol: 80 %
Description: DATA WERE COLLECTED AT DIFFERENT SYNCHROTRONS, SEE FIELD 'BEAMLINE'
Crystal growpH: 6.4 / Details: pH 6.4
Crystal grow
*PLUS
Method: batch method
Details: Fromme, P., (1998) Biochim. Biophys. Acta, 1365, 175.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mM11MgSO4
21 mMchlorophyll11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→60 Å / Num. obs: 89999 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.2
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 4.2 / % possible all: 78.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 4→60 Å / Details: NO REFINEMENT WAS CARRIED OUT ON THE MODEL
Refinement stepCycle: LAST / Resolution: 4→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 1828 0 3672
Refinement
*PLUS
Highest resolution: 4 Å / Lowest resolution: 60 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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