+Open data
-Basic information
Entry | Database: PDB / ID: 7xcq | ||||||
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Title | X-ray crystal structure of sperm whale myoglobin H64D mutant | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / SPERM WHALE MYOGLOBIN | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Lin, Y.W. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: X-ray crystal structure of sperm whale myoglobin H64D mutant Authors: 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 | 7xcq.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xcq.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xcq_validation.pdf.gz | 813.7 KB | Display | wwPDB validaton report |
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Full document | 7xcq_full_validation.pdf.gz | 814.9 KB | Display | |
Data in XML | 7xcq_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 7xcq_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/7xcq ftp://data.pdbj.org/pub/pdb/validation_reports/xc/7xcq | HTTPS FTP |
-Related structure data
Related structure data | 1mtjS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17343.088 Da / Num. of mol.: 1 / Mutation: H64D 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 / |
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: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 20645 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.08 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.027 / Net I/σ(I): 19.84 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 6.93 / Num. unique obs: 2037 / CC1/2: 0.99 / Rpim(I) all: 0.151 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MTJ Resolution: 1.6→24.15 Å / SU ML: 0.1167 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9162 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: 19.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→24.15 Å
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Refine LS restraints |
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LS refinement shell |
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