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Yorodumi- PDB-1m20: Crystal Structure of F35Y Mutant of Trypsin-solubilized Fragment ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m20 | ||||||
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Title | Crystal Structure of F35Y Mutant of Trypsin-solubilized Fragment of Cytochrome b5 | ||||||
Components | Cytochrome b5 | ||||||
Keywords | ELECTRON TRANSPORT / cytochrome b5 / trypsin-cleaved fragment / mutant F35Y | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Yao, P. / Wu, J. / Wang, Y.-H. / Sun, B.-Y. / Xia, Z.-X. / Huang, Z.-X. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2002 Title: X-ray crystallography, CD and kinetic studies revealed the essence of the abnormal behaviors of the cytochrome b5 Phe35-->Tyr mutant. Authors: Yao, P. / Wu, J. / Wang, Y.H. / Sun, B.Y. / Xia, Z.X. / 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 | 1m20.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m20.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 1m20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m20_validation.pdf.gz | 779.3 KB | Display | wwPDB validaton report |
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Full document | 1m20_full_validation.pdf.gz | 779.5 KB | Display | |
Data in XML | 1m20_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1m20_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/1m20 ftp://data.pdbj.org/pub/pdb/validation_reports/m2/1m20 | HTTPS FTP |
-Related structure data
Related structure data | 1es1S 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: 9491.380 Da / Num. of mol.: 1 / Fragment: trypsin-solubilized fragment / Mutation: F35Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pUC19 / 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: 2.75 Å3/Da / Density % sol: 55.2 % | ||||||||||||||||||
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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 ℃ | ||||||||||||||||||
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 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
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→19.91 Å / Num. all: 9129 / Num. obs: 8384 / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.061 |
Reflection shell | Resolution: 1.8→1.84 Å / Num. unique all: 511 / Rsym value: 0.315 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 9129 / % possible obs: 94.3 % / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 79.7 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 1ES1 Resolution: 1.8→19.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 589664.97 / 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: 39.0714 Å2 / ksol: 0.351386 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.193 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.302 / Rfactor Rwork: 0.306 |