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Yorodumi- PDB-3x34: Crystal structure of the reduced form of the solubilized domain o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x34 | ||||||
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Title | Crystal structure of the reduced form of the solubilized domain of porcine cytochrome b5 in form 1 crystal | ||||||
Components | Cytochrome b5 | ||||||
Keywords | ELECTRON TRANSPORT / HEME | ||||||
Function / homology | Function and homology information Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial outer membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.76 Å | ||||||
Authors | Hirano, Y. / Kimura, S. / Tamada, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: High-resolution crystal structures of the solubilized domain of porcine cytochrome b5. Authors: Hirano, Y. / Kimura, S. / Tamada, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x34.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x34.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 3x34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x34_validation.pdf.gz | 976.8 KB | Display | wwPDB validaton report |
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Full document | 3x34_full_validation.pdf.gz | 982.4 KB | Display | |
Data in XML | 3x34_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3x34_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/3x34 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/3x34 | HTTPS FTP |
-Related structure data
Related structure data | 3x32C 3x33C 3x35C 1cyoS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 10770.889 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP residues 1-94 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CYB5A, CYB5 / Plasmid: pCPb5 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00172 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24% PEG 1500, 4% 2-propanol, 0.1M calcium chloride, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.8 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2014 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 0.76→50 Å / Num. all: 99370 / Num. obs: 99196 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 67.4 |
Reflection shell | Resolution: 0.76→0.77 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 4.1 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CYO Resolution: 0.76→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 0.76→50 Å
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Refine LS restraints |
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