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Yorodumi- PDB-4pqc: A sperm whale myoglobin single mutant F43H Mb with native His93 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pqc | ||||||
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Title | A sperm whale myoglobin single mutant F43H Mb with native His93 coordination | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Structural Genomics / Enzyme Function Initiative / alpha helix bundle / nitrite reductase / native state | ||||||
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 / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å | ||||||
Authors | Ying-wu, L. / Xiang-shi, T. / Wei, L. | ||||||
Citation | Journal: ChemistryOpen / Year: 2015 Title: Regulating the coordination state of a heme protein by a designed distal hydrogen-bonding network. Authors: Du, J.F. / Li, W. / Li, L. / Wen, G.B. / Lin, Y.W. / Tan, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pqc.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pqc.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pqc_validation.pdf.gz | 813.5 KB | Display | wwPDB validaton report |
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Full document | 4pqc_full_validation.pdf.gz | 816.8 KB | Display | |
Data in XML | 4pqc_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 4pqc_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/4pqc ftp://data.pdbj.org/pub/pdb/validation_reports/pq/4pqc | 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: 17357.121 Da / Num. of mol.: 1 / Mutation: F43H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate, 30% w/v Polyethylene glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→30.65 Å / Num. all: 23101 / Num. obs: 22589 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.048 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.503→30.65 Å / SU ML: 0.28 / σ(F): 0.16 / Phase error: 19.56 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.645 Å2 / ksol: 0.401 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.503→30.65 Å
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Refine LS restraints |
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LS refinement shell |
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