+Open data
-Basic information
Entry | Database: PDB / ID: 1awp | ||||||
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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 / ubiquinol-cytochrome-c reductase activity / nitrite reductase (NO-forming) 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: 2 Å | ||||||
Authors | Wang, X. / Zhang, X. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: The reduction potential of cytochrome b5 is modulated by its exposed heme edge. Authors: Rivera, M. / Seetharaman, R. / Girdhar, D. / Wirtz, M. / Zhang, X. / Wang, X. / White, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1awp.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1awp.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 1awp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1awp_validation.pdf.gz | 523 KB | Display | wwPDB validaton report |
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Full document | 1awp_full_validation.pdf.gz | 528.1 KB | Display | |
Data in XML | 1awp_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1awp_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/1awp ftp://data.pdbj.org/pub/pdb/validation_reports/aw/1awp | HTTPS FTP |
-Related structure data
Related structure data | 1b5mS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.54813, 0.5997, 0.58302), Vector: |
-Components
#1: Protein | Mass: 10419.405 Da / Num. of mol.: 2 / Fragment: WATER SOLUBLE DOMAIN / Mutation: V45L, V61L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: HEPATOCYTE / Cell line: BL21 / Cellular location: OUTER MITOCHONDRIAL MEMBRANE / Gene: POTENTIAL / Organ: LIVER / Organelle: MITOCHONDRION / Plasmid: PET 11A / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASMIC SPACE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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: 2.7 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1997 |
Radiation | Monochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→10 Å / Num. obs: 16374 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.075 / Net I/σ(I): 32.42 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.18 % / Mean I/σ(I) obs: 3.41 / Rsym value: 0.274 / % possible all: 92.5 |
Reflection | *PLUS Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 84.7 % / Rmerge(I) obs: 0.274 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B5M Resolution: 2→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: NCS RESTRAINTS WERE USED IN INITIAL STEP OF REFINEMENT. BULK SOLVENT MODELING METHOD WAS USED.
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Displacement parameters | Biso mean: 37.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2259 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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