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Yorodumi- PDB-1es1: CRYSTAL STRUCTURE OF VAL61HIS MUTANT OF TRYPSIN-SOLUBILIZED FRAGM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1es1 | |||||||||
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Title | CRYSTAL STRUCTURE OF VAL61HIS MUTANT OF TRYPSIN-SOLUBILIZED FRAGMENT OF CYTOCHROME B5 | |||||||||
Components | CYTOCHROME B5 | |||||||||
Keywords | ELECTRON TRANSPORT / cytochrome b5 / trypsin-cleaved fragment / mutant Val61His / crystal structure / structure comparison with the wild type fragment | |||||||||
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 | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | |||||||||
Authors | Wu, J. / Gan, J.-H. / Xia, Z.-X. / Wang, Y.-H. / Wang, W.-H. / Xue, L.-L. / Xie, Y. / Huang, Z.-X. | |||||||||
Citation | Journal: Proteins / Year: 2000 Title: Crystal structure of recombinant trypsin-solubilized fragment of cytochrome b(5) and the structural comparison with Val61His mutant. Authors: Wu, J. / Gan, J.H. / Xia, Z.X. / Wang, Y.H. / Wang, W.H. / Xue, L.L. / Xie, Y. / Huang, Z.X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1es1.cif.gz | 32.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1es1.ent.gz | 20.7 KB | Display | PDB format |
PDBx/mmJSON format | 1es1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1es1_validation.pdf.gz | 765.4 KB | Display | wwPDB validaton report |
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Full document | 1es1_full_validation.pdf.gz | 766 KB | Display | |
Data in XML | 1es1_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1es1_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1es1 ftp://data.pdbj.org/pub/pdb/validation_reports/es/1es1 | HTTPS FTP |
-Related 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: 9514.396 Da / Num. of mol.: 1 / Fragment: TRYPSIN-SOLUBILIZED FRAGMENT / Mutation: VAL61HIS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00171 |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 2.74 Å3/Da / Density % sol: 55.13 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: phosphate buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SEALED TUBE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→12 Å / Num. obs: 5579 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 1.93 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 1.62 % / Rmerge(I) obs: 0.232 / % possible all: 79.5 |
-Processing
Software |
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Refinement | Resolution: 2.1→12 Å / σ(F): 0 / Stereochemistry target values: CNS library
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Refinement step | Cycle: LAST / Resolution: 2.1→12 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 0 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |