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Yorodumi- PDB-1bz6: ATOMIC RESOLUTION CRYSTAL STRUCTURE AQUOMET-MYOGLOBIN FROM SPERM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bz6 | ||||||
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Title | ATOMIC RESOLUTION CRYSTAL STRUCTURE AQUOMET-MYOGLOBIN FROM SPERM WHALE AT ROOM TEMPERATURE | ||||||
Components | PROTEIN (MYOGLOBIN) | ||||||
Keywords | OXYGEN STORAGE / OXYGEN TRANSPORT / RESPIRATORY PROTEIN / HEME / ATOMIC RESOLUTION | ||||||
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: 1.2 Å | ||||||
Authors | Popov, A.N. / Kachalova, G.S. / Bartunik, H.D. | ||||||
Citation | Journal: Science / Year: 1999 Title: A steric mechanism for inhibition of CO binding to heme proteins. Authors: Kachalova, G.S. / Popov, A.N. / Bartunik, H.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bz6.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bz6.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bz6_validation.pdf.gz | 805.8 KB | Display | wwPDB validaton report |
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Full document | 1bz6_full_validation.pdf.gz | 807.6 KB | Display | |
Data in XML | 1bz6_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 1bz6_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bz6 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bz6 | HTTPS FTP |
-Related structure data
Related structure data | 1bzpC 1bzrC 4mbnS S: Starting model for refinement C: citing same article (ref.) |
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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: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Tissue: MUSCLE / References: UniProt: P02185 | ||||
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#2: Chemical | ChemComp-SO4 / #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: 1.94 Å3/Da / Density % sol: 36.71 % |
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Crystal grow | pH: 6 Details: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM SULPHATE, 0.1 M POTASSIUM PHOSPHATE, pH 6.0 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→60 Å / Num. obs: 41547 / % possible obs: 99.4 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 6.6 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 564343 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MBN Resolution: 1.2→12 Å / Num. parameters: 14814 / Num. restraintsaints: 20313 / σ(F): 0 StereochEM target val spec case: HEME - PARAMETERS BASED ON CSD Stereochemistry target values: ENGH AND HUBER Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON ATOM AND HEME PLANARITY
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 81 / Occupancy sum hydrogen: 1034.6 / Occupancy sum non hydrogen: 1436.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→12 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.112 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |