+Open data
-Basic information
Entry | Database: PDB / ID: 3nml | ||||||
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Title | Sperm whale myoglobin mutant H64W carbonmonoxy-form | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / Myoglobin / ligand migration pathways | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å | ||||||
Authors | Birukou, I. / Soman, J. / Olson, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Blocking the gate to ligand entry in human hemoglobin. Authors: Birukou, I. / Soman, J. / Olson, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nml.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nml.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 3nml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nml_validation.pdf.gz | 795 KB | Display | wwPDB validaton report |
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Full document | 3nml_full_validation.pdf.gz | 796.7 KB | Display | |
Data in XML | 3nml_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3nml_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/3nml ftp://data.pdbj.org/pub/pdb/validation_reports/nm/3nml | HTTPS FTP |
-Related structure data
Related structure data | 3nl7C 3nmmC 3ogbC 2mbwS 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: 17413.225 Da / Num. of mol.: 1 / Mutation: H65W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): Phage resistant TB1 / References: UniProt: P02185 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-CMO / | ||
#4: Chemical | #5: 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: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 293 K / Method: batch method / pH: 9 Details: Protein solution (20mg/ml protein in 0.02m Tris-HCl ph9.0) mixed with mother liquor (3.2m ammonium sulphate, 0.05m tris-hcl, ph9.0) for final concentrations of 2.5m ammonium sulphate, Batch ...Details: Protein solution (20mg/ml protein in 0.02m Tris-HCl ph9.0) mixed with mother liquor (3.2m ammonium sulphate, 0.05m tris-hcl, ph9.0) for final concentrations of 2.5m ammonium sulphate, Batch Method, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 10, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.68→41.59 Å / Num. obs: 19145 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 3.71 % / Rmerge(I) obs: 0.041 / Χ2: 0.97 / Net I/σ(I): 19.7 / Scaling rejects: 537 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Method rotation: fast direct / Method translation: &STRIP%trans_method |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2MBW Resolution: 1.68→22.711 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 16.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.308 Å2 / ksol: 0.419 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.35 Å2 / Biso mean: 20.653 Å2 / Biso min: 6.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→22.711 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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