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Yorodumi- PDB-2bc5: Crystal structure of E. coli cytochrome b562 with engineered c-ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bc5 | |||||||||
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Title | Crystal structure of E. coli cytochrome b562 with engineered c-type heme linkages | |||||||||
Components | Soluble cytochrome b562 | |||||||||
Keywords | ELECTRON TRANSPORT / Four-Helix Bundle / K59W / R98C and Y101C mutations | |||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Faraone-Mennella, J. / Tezcan, F.A. / Gray, H.B. / Winkler, J.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Stability and Folding Kinetics of Structurally Characterized Cytochrome c-b(562). Authors: Faraone-Mennella, J. / Tezcan, F.A. / Gray, H.B. / Winkler, J.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bc5.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bc5.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 2bc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/2bc5 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/2bc5 | HTTPS FTP |
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-Related structure data
Related structure data | 256bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 11742.189 Da / Num. of mol.: 4 / Mutation: K59W, R98C, Y101C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pETcb562 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ABE7 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HEC / #4: 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 | Density Matthews: 2.09 Å3/Da / Density % sol: 41.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 70% ammonium sulfate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Nov 1, 2004 |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→24.4 Å / Num. all: 19341 / Num. obs: 19081 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.25→2.3 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.2 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 256B Resolution: 2.25→24.4 Å / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.38 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.27 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→24.4 Å
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Refine LS restraints |
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Xplor file |
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