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Yorodumi- PDB-1wvp: Structure of chemically modified myoglobin with distal N-tetrazol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wvp | ||||||
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Title | Structure of chemically modified myoglobin with distal N-tetrazolyl-histidine E7(64) | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / myoglobin / HEMOPROTEIN / Tetrazole / chemical modification / distal HisE7 / oxygen carrier / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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: 1.53 Å | ||||||
Authors | Makino, M. / Sugimoto, H. / Kamiya, N. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1991 Title: Heme environmental structure of a novel artificial myoglobin with a closed heme pocket: site-specific chemical modification producing distal N-tetrazolylhistidine E7 by cyanogen bromide and azide ion Authors: Kamiya, N. / Shiro, Y. / Iwata, T. / Iizuka, T. / Iwasaki, H. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Specific modification of structure and property of myoglobin by the formation of tetrazolylhistidine 64(E7). Reaction of the modified myoglobin with molecular oxygen Authors: Shiro, Y. / Iwata, T. / Makino, R. / Fujii, M. / Isogai, Y. / Iizuka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wvp.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wvp.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wvp_validation.pdf.gz | 828.2 KB | Display | wwPDB validaton report |
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Full document | 1wvp_full_validation.pdf.gz | 829.8 KB | Display | |
Data in XML | 1wvp_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1wvp_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvp ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvp | HTTPS FTP |
-Related structure data
Related structure data | 1a6kS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17285.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Tissue: skeletal muscle / References: UniProt: P02185 | ||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #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: 2.3 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 293 K / Method: batch / pH: 7 Details: Ammonium Sulfate, Phosphate, pH 7.0, batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 16, 2003 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. all: 24645 / Num. obs: 24611 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.94 Å2 / Rsym value: 0.05 / Net I/σ(I): 45.95 |
Reflection shell | Resolution: 1.53→1.58 Å / Mean I/σ(I) obs: 9.37 / Num. unique all: 2366 / Rsym value: 0.345 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A6K Resolution: 1.53→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.076 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.043 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Total num. of bins used: 20
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