+Open data
-Basic information
Entry | Database: PDB / ID: 1eue | ||||||
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Title | RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 | ||||||
Components | CYTOCHROME B5 | ||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME / HEME | ||||||
Function / homology | Function and homology information Sphingolipid de novo biosynthesis / Phase I - Functionalization of compounds / nitric-oxide synthase complex / nitrite reductase (NO-forming) activity / ubiquinol-cytochrome-c reductase activity / enzyme activator activity / nitric oxide biosynthetic process / mitochondrial outer membrane / intracellular membrane-bounded organelle / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Oganesyan, V. / Zhang, X. | ||||||
Citation | Journal: FARADAY DISC.CHEM.SOC / Year: 2001 Title: Modulation of redox potential in electron transfer proteins: effects of complex formation on the active site microenvironment of cytochrome b5. Authors: Wirtz, M. / Oganesyan, V. / Zhang, X. / Studer, J. / Rivera, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eue.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eue.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 1eue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/1eue ftp://data.pdbj.org/pub/pdb/validation_reports/eu/1eue | HTTPS FTP |
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-Related structure data
Related structure data | 1awpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9845.826 Da / Num. of mol.: 2 / Fragment: WATER SOLUBLE DOMAIN / Mutation: V45I, V61I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: HEPATOCYTE Cellular location: OUTER MITOCHONDRIAL MEMBRANEMitochondrion Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PET 11A / Cellular location (production host): PERIPLASMIC SPACE / Production host: Escherichia coli (E. coli) / References: UniProt: P04166 #2: Chemical | #3: 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: 3 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 20% PEG 8000, 0.2 M magnesium acetate, 0.1 M PIPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: drop solution is mixed 1:1 by volume with precipitant solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2000 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24.2 Å / Num. obs: 21091 / % possible obs: 93 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 91.8 |
Reflection shell | *PLUS % possible obs: 91.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AWP Resolution: 1.8→11.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1103526.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.14 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→11.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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