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Yorodumi- PDB-5hlx: X-ray crystal structure of met F43H/H64A sperm whale myoglobin in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hlx | ||||||
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Title | X-ray crystal structure of met F43H/H64A sperm whale myoglobin in complex with nitrite | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / 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: 1.5 Å | ||||||
Authors | Yuan, H. | ||||||
Citation | Journal: Nitric Oxide / Year: 2016 Title: Regulating the nitrite reductase activity of myoglobin by redesigning the heme active center Authors: Wu, L.B. / Yuan, H. / Gao, S.Q. / You, Y. / Nie, C.M. / 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 | 5hlx.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hlx.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 5hlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hlx_validation.pdf.gz | 858.5 KB | Display | wwPDB validaton report |
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Full document | 5hlx_full_validation.pdf.gz | 860.5 KB | Display | |
Data in XML | 5hlx_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 5hlx_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/5hlx ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hlx | HTTPS FTP |
-Related structure data
Related structure data | 5hlqC 5hluC 4of9S C: citing same article (ref.) 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: 17158.855 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: F43H/H64A 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: Chemical | #4: 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: 2.22 Å3/Da / Density % sol: 44.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30%(w/v) Polyethylene glycol 8,000, 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Jan 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 25250 / % possible obs: 99.8 % / Redundancy: 6.4 % / Net I/σ(I): 20.08 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 20.1 / Rsym value: 0.099 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OF9 Resolution: 1.5→35.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.955 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.775 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→35.37 Å
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Refine LS restraints |
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