+Open data
-Basic information
Entry | Database: PDB / ID: 2jbl | ||||||||||||
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Title | PHOTOSYNTHETIC REACTION CENTER FROM BLASTOCHLORIS VIRIDIS | ||||||||||||
Components |
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Keywords | ELECTRON TRANSPORT / CHROMOPHORE / FORMYLATION / CHLOROPHYLL / LIPOPROTEIN / STIGMATELLIN / METAL-BINDING / TRANSMEMBRANE / IRON / HEME / MEMBRANE / TRANSPORT / MAGNESIUM / PHOTOSYNTHESIS / REACTION CENTER / BACTERIOCHLOROPHYLL / PHOTOSYNTHETIC REACTION CENTER | ||||||||||||
Function / homology | Function and homology information plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | BLASTOCHLORIS VIRIDIS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Lancaster, C.R.D. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome Bc(1) Complex. Authors: Lancaster, C.R.D. / Hunte, C. / Kelley, J. / Trumpower, B.L. / Ditchfield, R. #1: Journal: J.Biol.Chem. / Year: 2000 Title: Structural Basis of the Drastically Increased Initial Electron Transfer Rate in the Reaction Center from a Rhodopseudomonas Viridis Mutant Described at 2.00-A Resolution Authors: Lancaster, C.R.D. / Bibikova, M. / Sabatino, P. / Oesterhelt, D. / Michel, H. #2: Journal: J.Mol.Biol. / Year: 1999 Title: Refined Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to a New Model of the Bound Carotenoid Authors: Lancaster, C.R. / Michel, H. #3: Journal: Biochim.Biophys.Acta / Year: 1998 Title: Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications Authors: Lancaster, C.R.D. #4: Journal: Structure / Year: 1997 Title: The Coupling of Light-Induced Electron Transfer and Proton Uptake as Derived from Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis Modified at the Binding Site of the Secondary Quinone, Qb Authors: Lancaster, C.R. / Michel, H. #5: Journal: J.Mol.Biol. / Year: 1995 Title: Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas Viridis Authors: Deisenhofer, J. / Epp, O. / Sinning, I. / Michel, H. #6: Journal: Science / Year: 1989 Title: The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis Authors: Deisenhofer, J. / Michel, H. #7: Journal: Nature / Year: 1985 Title: Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H. #8: Journal: J.Mol.Biol. / Year: 1984 Title: X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 A Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H. #9: Journal: J.Mol.Biol. / Year: 1982 Title: Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis Authors: Michel, H. | ||||||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jbl.cif.gz | 287.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jbl.ent.gz | 224.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jbl_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 2jbl_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 2jbl_validation.xml.gz | 52 KB | Display | |
Data in CIF | 2jbl_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jbl ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jbl | HTTPS FTP |
-Related structure data
Related structure data | 2ibzC 4prc S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules C
#1: Protein | Mass: 39419.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM 133) / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P07173 |
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-REACTION CENTER PROTEIN ... , 3 types, 3 molecules HLM
#2: Protein | Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM 133) / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06008 |
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#3: Protein | Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM 133) / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06009 |
#4: Protein | Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS (DSM 133) / Source: (natural) BLASTOCHLORIS VIRIDIS (bacteria) / References: UniProt: P06010 |
-Non-polymers , 10 types, 366 molecules
#5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-LDA / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-BCB / #9: Chemical | #10: Chemical | ChemComp-SMA / | #11: Chemical | ChemComp-FE / | #12: Chemical | ChemComp-MQ7 / | #13: Chemical | ChemComp-NS5 / | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 74.28 % |
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Crystal grow | pH: 6 / Details: pH 6.00 |
-Data collection
Diffraction | Mean temperature: 263 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 13, 1992 / Details: FOCUSING MIRROR |
Radiation | Monochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→26.56 Å / Num. obs: 103499 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.6 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4PRC 4prc Resolution: 2.4→26.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3307055.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.1587 Å2 / ksol: 0.285982 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→26.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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