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Yorodumi- PDB-2fyn: Crystal Structure Analysis of the double mutant Rhodobacter Sphae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fyn | ||||||
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Title | Crystal Structure Analysis of the double mutant Rhodobacter Sphaeroides bc1 complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Transmembrane helices / functional dimer | ||||||
Function / homology | Function and homology information respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / : / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Esser, L. / Xia, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex. Authors: Esser, L. / Gong, X. / Yang, S. / Yu, L. / Yu, C.A. / Xia, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fyn.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2fyn.ent.gz | 850.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fyn_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 2fyn_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 2fyn_validation.xml.gz | 134.9 KB | Display | |
Data in CIF | 2fyn_validation.cif.gz | 190.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/2fyn ftp://data.pdbj.org/pub/pdb/validation_reports/fy/2fyn | HTTPS FTP |
-Related structure data
Related structure data | 2fyuC 1qcrS 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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2 |
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3 |
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Unit cell |
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Details | the asymmetric unit contains three independent dimers (biological assembly) |
-Components
-Protein , 3 types, 18 molecules ADGJMPBEHKNQCFILOR
#1: Protein | Mass: 50157.539 Da / Num. of mol.: 6 / Fragment: cytochrome b / Mutation: S287R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petB, fbcB / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q02761 #2: Protein | Mass: 29373.953 Da / Num. of mol.: 6 / Fragment: cytochrome c1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petC, fbcC / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q02760 #3: Protein | Mass: 19916.322 Da / Num. of mol.: 6 / Fragment: Rieske Iron sulfur protein / Mutation: V135S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petA, fbcF / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q02762, quinol-cytochrome-c reductase |
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-Non-polymers , 4 types, 36 molecules
#4: Chemical | ChemComp-HEM / #5: Chemical | ChemComp-SMA / #6: Chemical | ChemComp-LOP / ( #7: Chemical | ChemComp-FES / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.6 % |
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Crystal grow | Temperature: 288.2 K / Method: evaporation / pH: 7.5 Details: 10% PEG400, 0.2 M NaCl, 0.2 M Histidine, 0.1M Tris, 10% Glycerol, 5 mM NaN3, 10% Glycerol, 2mM DHPC, 0.5% beta-octyl glucopyranoside, 0.06% sucrose monocarprate, 10mM Sr(NO3)2, pH 7.5, ...Details: 10% PEG400, 0.2 M NaCl, 0.2 M Histidine, 0.1M Tris, 10% Glycerol, 5 mM NaN3, 10% Glycerol, 2mM DHPC, 0.5% beta-octyl glucopyranoside, 0.06% sucrose monocarprate, 10mM Sr(NO3)2, pH 7.5, EVAPORATION, temperature 288.2K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. all: 160039 / Num. obs: 155528 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.4 | ||||||||||||||||||
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.37 / Num. unique all: 13841 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1qcr Resolution: 3.2→18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 111061.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.4667 Å2 / ksol: 0.285271 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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