+Open data
-Basic information
Entry | Database: PDB / ID: 4h07 | |||||||||
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Title | Complex of G65T Myoglobin with Phenol in its Proximal Cavity | |||||||||
Components | Myoglobin | |||||||||
Keywords | OXYGEN TRANSPORT | |||||||||
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 / Resolution: 1.14 Å | |||||||||
Authors | Lebioda, L. / Lovelace, L.L. / Celeste, L.R. / Huang, X. / Wang, C. / Shengfang, S. / Dawson, J.H. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Complex of myoglobin with phenol bound in a proximal cavity. Authors: Huang, X. / Wang, C. / Celeste, L.R. / Lovelace, L.L. / Sun, S. / Dawson, J.H. / Lebioda, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h07.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h07.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 4h07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h07_validation.pdf.gz | 828.3 KB | Display | wwPDB validaton report |
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Full document | 4h07_full_validation.pdf.gz | 832.4 KB | Display | |
Data in XML | 4h07_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 4h07_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/4h07 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/4h07 | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17410.199 Da / Num. of mol.: 1 / Mutation: G65T 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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-Non-polymers , 5 types, 241 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-IPH / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: 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: 3.06 Å3/Da / Density % sol: 59.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.6M AS, 50mM Tris 8.5, 1mM EDTA, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.14→50 Å / Num. obs: 76906 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4.2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.052 / Χ2: 1.246 / Net I/σ(I): 13.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.14→39.13 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1613 / WRfactor Rwork: 0.1404 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.9433 / SU B: 0.589 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0249 / SU Rfree: 0.0257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.92 Å2 / Biso mean: 12.9702 Å2 / Biso min: 4.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.14→39.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.14→1.17 Å / Total num. of bins used: 20
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