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Yorodumi- PDB-1f6n: CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT REACTION CENTER PRO L209... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f6n | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT REACTION CENTER PRO L209-> TYR FROM THE PHOTOSYNTHETIC PURPLE BACTERIUM RHODOBACTER SPHAEROIDES | ||||||
Components | (REACTION CENTER PROTEIN ...) x 3 | ||||||
Keywords | PHOTOSYNTHESIS / amino acid displacement | ||||||
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 / membrane => GO:0016020 / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Kuglstatter, A. / Ermler, U. / Michel, H. / Baciou, L. / Fritzsch, G. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: X-ray structure analyses of photosynthetic reaction center variants from Rhodobacter sphaeroides: structural changes induced by point mutations at position L209 modulate electron and proton transfer. Authors: Kuglstatter, A. / Ermler, U. / Michel, H. / Baciou, L. / Fritzsch, G. #1: Journal: Biochemistry / Year: 1995 Title: Interruption of the Water Chain in the Reaction Center from Rhodobacter sphaeroides Reduces the Rates of the Proton Uptake and of the Second Electron Transfer to Q(B) Authors: Baciou, L. / Michel, H. #2: Journal: Biochemistry / Year: 1999 Title: In Rhodobacter sphaeroides Reaction Centers, Mutation of Proline L209 to Aromatic Residues in the Vicinity of a Water Channel Alters the Dynamic Coupling between Electron and Proton Transfer Processes. Authors: Tandori, J. / Sebban, P. / Michel, H. / Baciou, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f6n.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f6n.ent.gz | 153.8 KB | Display | PDB format |
PDBx/mmJSON format | 1f6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f6n_validation.pdf.gz | 813 KB | Display | wwPDB validaton report |
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Full document | 1f6n_full_validation.pdf.gz | 861.9 KB | Display | |
Data in XML | 1f6n_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 1f6n_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/1f6n ftp://data.pdbj.org/pub/pdb/validation_reports/f6/1f6n | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-REACTION CENTER PROTEIN ... , 3 types, 3 molecules LMH
#1: Protein | Mass: 31412.447 Da / Num. of mol.: 1 / Mutation: P209Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Plasmid: PRK404 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02954, UniProt: P0C0Y8*PLUS |
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#2: Protein | Mass: 34398.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Plasmid: PRK404 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P02953, UniProt: P0C0Y9*PLUS |
#3: Protein | Mass: 28066.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Plasmid: PRK404 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P11846, UniProt: P0C0Y7*PLUS |
-Non-polymers , 8 types, 114 molecules
#4: Chemical | ChemComp-BCL / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-LDA / #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-PO4 / | #10: Chemical | ChemComp-SPO / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: potassium phosphate, 1,2,3-heptanetriol, 1,2,3-hexanetriol, LDAO, NaCl, dioxane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K | ||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / Details: Fritzsch, G.,(1998) Methods Enzymol., 297, 57. | ||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 54353 / Num. obs: 52164 / % possible obs: 96 % / Observed criterion σ(I): -1 / Redundancy: 1.7 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.27 / Num. unique all: 5141 / % possible all: 95.4 |
Reflection shell | *PLUS % possible obs: 95.4 % |
-Processing
Software |
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Refinement | Resolution: 2.8→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1025017.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: Engh & Huber, Treutlein et al.,
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Displacement parameters | Biso mean: 68.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.251 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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