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- PDB-2pps: PHOTOSYNTHETIC REACTION CENTER AND CORE ANTENNA SYSTEM (TRIMERIC)... -

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Basic information

Entry
Database: PDB / ID: 2pps
TitlePHOTOSYNTHETIC REACTION CENTER AND CORE ANTENNA SYSTEM (TRIMERIC), ALPHA CARBON ONLY
Components(PHOTOSYSTEM I) x 6
KeywordsPHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / OXYGENIC PHOTOSYNTHESIS / CORE-ANTENNA LIGHT-HARVESTING SYSTEM / THERMOPHILIC CYANOBACTERIUM / HELIX-BUNDLE MEMBRANE PROTEIN
Function / homologyCHLOROPHYLL A / PHYLLOQUINONE / IRON/SULFUR CLUSTER
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 4 Å
AuthorsKrauss, N. / Schubert, W.-D. / Klukas, O. / Fromme, P. / Witt, H.T. / Saenger, W.
Citation
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.
#1: 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.
#2: Journal: Photosynthesis : From Light to Biosphere : Proceedings of the Xth International Photosynthesis Congress, Montpellier, France, 20-25 August 1995
Year: 1995
Title: Present State of the Crystal Structure Analysis of Photosystem I at 4.5 A Resolution
Authors: Schubert, W.D. / Klukas, O. / Krauss, N. / Saenger, W. / Fromme, P. / Witt, H.T.
#3: 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.
#4: 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
DepositionMay 27, 1997Processing site: BNL
SupersessionMay 27, 1998ID: 1PPS
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_validate_chiral / software / 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 / _software.name / _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 I
B: PHOTOSYSTEM I
L: PHOTOSYSTEM I
K: PHOTOSYSTEM I
F: PHOTOSYSTEM I
C: PHOTOSYSTEM I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,38899
Polymers116,3616
Non-polymers81,02693
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,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 , 6 types, 6 molecules ABLKFC

#1: Protein PHOTOSYSTEM I / / PSI / SYSTEM I OF OXYGENIC PHOTOSYNTHESIS / Coordinate model: Cα atoms only


Mass: 40698.164 Da / Num. of mol.: 1
Fragment: THE PSI-PROTOMER IS A COMPLEX OF PSAA, PSAB, PSAC, PSAD, PSAE, PSAF, PSAI, PSAJ, PSAK, PSAL, PSAM
Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANEThylakoid
#2: Protein PHOTOSYSTEM I / / PSI / SYSTEM I OF OXYGENIC PHOTOSYNTHESIS / Coordinate model: Cα atoms only


Mass: 42825.812 Da / Num. of mol.: 1
Fragment: THE PSI-PROTOMER IS A COMPLEX OF PSAA, PSAB, PSAC, PSAD, PSAE, PSAF, PSAI, PSAJ, PSAK, PSAL, PSAM
Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANEThylakoid
#3: Protein PHOTOSYSTEM I / / PSI / SYSTEM I OF OXYGENIC PHOTOSYNTHESIS / Coordinate model: Cα atoms only


Mass: 9464.658 Da / Num. of mol.: 1
Fragment: THE PSI-PROTOMER IS A COMPLEX OF PSAA, PSAB, PSAC, PSAD, PSAE, PSAF, PSAI, PSAJ, PSAK, PSAL, PSAM
Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANEThylakoid
#4: Protein PHOTOSYSTEM I / / PSI / SYSTEM I OF OXYGENIC PHOTOSYNTHESIS / Coordinate model: Cα atoms only


Mass: 5464.728 Da / Num. of mol.: 1
Fragment: THE PSI-PROTOMER IS A COMPLEX OF PSAA, PSAB, PSAC, PSAD, PSAE, PSAF, PSAI, PSAJ, PSAK, PSAL, PSAM
Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANEThylakoid
#5: Protein PHOTOSYSTEM I / / PSI / SYSTEM I OF OXYGENIC PHOTOSYNTHESIS / Coordinate model: Cα atoms only


Mass: 11081.651 Da / Num. of mol.: 1
Fragment: THE PSI-PROTOMER IS A COMPLEX OF PSAA, PSAB, PSAC, PSAD, PSAE, PSAF, PSAI, PSAJ, PSAK, PSAL, PSAM
Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANEThylakoid
#6: Protein PHOTOSYSTEM I / / PSI / SYSTEM I OF OXYGENIC PHOTOSYNTHESIS / Coordinate model: Cα atoms only


Mass: 6826.406 Da / Num. of mol.: 1
Fragment: THE PSI-PROTOMER IS A COMPLEX OF PSAA, PSAB, PSAC, PSAD, PSAE, PSAF, PSAI, PSAJ, PSAK, PSAL, PSAM
Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANEThylakoid

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Non-polymers , 3 types, 93 molecules

#7: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#8: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H46O2
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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 AND PSAJ, POSSIBLY 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: 1

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Sample preparation

CrystalDensity % sol: 80 %
Crystal growpH: 6.4
Details: PROTEIN CONCENTRATION:80 MG/ML METHOD: MICRODIALYSIS BUFFER: 0.02% BETA-DODECYLMALTOSIDE, 5 MM MES, PH 6.4
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
180 mg/mlprotein11
310 mM11MgSO4
2MES11

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1993 / Details: FLAT SEGMENTED MIRROR
RadiationMonochromator: BENT CYLINDRICAL GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.85→34.9 Å / Num. obs: 69153 / % possible obs: 94.4 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.085 / Rsym value: 0.102 / Net I/σ(I): 6.4
Reflection shellResolution: 3.85→3.95 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.173 / % possible all: 81.3
Reflection shell
*PLUS
% possible obs: 81.3 % / Rmerge(I) obs: 0.173

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Processing

Software
NameVersionClassification
MLPHAREphasing
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MIR / Highest resolution: 4 Å
Details: MODEL STRUCTURE IS BASED ON 4.0 ANGSTROM MIR MAP. THERE WAS NO REFINEMENT DUE TO LIMITED RESOLUTION.
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 2250 0 3616

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