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Yorodumi- PDB-1c51: PHOTOSYNTHETIC REACTION CENTER AND CORE ANTENNA SYSTEM (TRIMERIC)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c51 | |||||||||
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Title | PHOTOSYNTHETIC REACTION CENTER AND CORE ANTENNA SYSTEM (TRIMERIC), ALPHA CARBON ONLY | |||||||||
Components | (PROTEIN (PHOTOSYSTEM I: SUBUNIT ...) x 8 | |||||||||
Keywords | PHOTOSYNTHESIS/ELECTRON TRANSPORT / PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / OXYGENIC PHOTOSYNTHESIS / CORE- ANTENNA LIGHT-HARVESTING SYSTEM / THERMOPHILIC CYANOBACTERIUM / HELIX-BUNDLE MEMBRANE PROTEIN / PHOTOSYNTHESIS-ELECTRON TRANSPORT COMPLEX | |||||||||
Function / homology | CHLOROPHYLL A / PHYLLOQUINONE / IRON/SULFUR CLUSTER Function and homology information | |||||||||
Biological species | Synechococcus elongatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4 Å | |||||||||
Authors | Klukas, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c51.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c51.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 1c51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c51_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 1c51_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 1c51_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1c51_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/1c51 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/1c51 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-PROTEIN (PHOTOSYSTEM I: SUBUNIT ... , 8 types, 8 molecules ABCDEFKL
#1: Protein | Mass: 50825.766 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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#2: Protein | 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 | 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 | 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 | 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 | 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 | 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 | Mass: 10230.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria) / Cellular location: THYLAKOID MEMBRANE |
-Non-polymers , 3 types, 77 molecules
#9: Chemical | ChemComp-CLA / #10: Chemical | #11: Chemical | |
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-Details
Compound details | CHAIN 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 TRIMERIZAT |
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Nonpolymer details | THE ATOM NAMING OF THE CHLOROPHYLL MOLECULES IS ARBITRARY IN THE SENSE THAT THE AUTHORS DO NOT WISH ...THE ATOM NAMING OF THE CHLOROPHYL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 5.8 Å3/Da / Density % sol: 80 % Description: DATA WERE COLLECTED AT DIFFERENT SYNCHROTRONS, SEE FIELD 'BEAMLINE' | ||||||||||||||||||
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Crystal grow | pH: 6.4 / Details: pH 6.4 | ||||||||||||||||||
Crystal grow | *PLUS Method: batch methodDetails: Fromme, P., (1998) Biochim. Biophys. Acta, 1365, 175. | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.5→3.56 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 4.2 / % possible all: 78.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 4→60 Å / Details: NO REFINEMENT WAS CARRIED OUT ON THE MODEL | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 4→60 Å
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Refinement | *PLUS Highest resolution: 4 Å / Lowest resolution: 60 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |