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Yorodumi- PDB-7cez: An x-ray structure of G5K/Q8K/A19K/V21K Mb mutant with a positive... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cez | ||||||
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Title | An x-ray structure of G5K/Q8K/A19K/V21K Mb mutant with a positive charge | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / SPERM WHALE / MYOGLOBIN | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter macrocephalus (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Yuan, H. / Lin, Y.W. | ||||||
Citation | Journal: To Be Published Title: An x-ray structure of G5K/Q8K/A19K/V21K Mb mutant with a positive charge Authors: Yuan, H. / Lin, Y.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cez.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cez.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 7cez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7cez ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7cez | HTTPS FTP |
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-Related structure data
Related structure data | 6krcS 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: 17527.477 Da / Num. of mol.: 1 / Mutation: G5K,Q8K,A19K,V21K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter macrocephalus (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 8000, 0.2 M magnesium chloride,0.1 M sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→50 Å / Num. obs: 22117 / % possible obs: 99.7 % / Redundancy: 9.4 % / Biso Wilson estimate: 13.24 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.57→1.6 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1027 / Rpim(I) all: 0.188 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KRC Resolution: 1.57→30.47 Å / SU ML: 0.1439 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.4805 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→30.47 Å
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Refine LS restraints |
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LS refinement shell |
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