+Open data
-Basic information
Entry | Database: PDB / ID: 1a6m | ||||||
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Title | OXY-MYOGLOBIN, ATOMIC RESOLUTION | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / HEME PROTEIN / MODEL COMPOUNDS / OXYGEN STORAGE / LIGAND BINDING GEOMETRY / CONFORMATIONAL SUBSTATES | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Vojtechovsky, J. / Chu, K. / Berendzen, J. / Sweet, R.M. / Schlichting, I. | ||||||
Citation | Journal: Biophys.J. / Year: 1999 Title: Crystal structures of myoglobin-ligand complexes at near-atomic resolution. Authors: Vojtechovsky, J. / Chu, K. / Berendzen, J. / Sweet, R.M. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a6m.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6m.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 1a6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6m ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6m | HTTPS FTP |
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-Related structure data
Related structure data | 1a6gC 1a6kC 1a6nC 1mbcS 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: 17049.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-OXY / | #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: 1.9 Å3/Da / Density % sol: 36 % | ||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.84 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 67676 / % possible obs: 97 % / Observed criterion σ(I): -3 / Rsym value: 0.057 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1→1.1 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.232 / % possible all: 88 |
Reflection | *PLUS Num. measured all: 530931 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 88 % / Rmerge(I) obs: 0.232 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MBC Resolution: 1→8 Å / Num. parameters: 14251 / Num. restraintsaints: 18357 / Cross valid method: FREE R-VALUE StereochEM target val spec case: HEME - PARAMETERS BASED ON CSD Stereochemistry target values: ENGH & HUBER Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF THE HEME. BAYESIAN WEIGHTING WAS APPLIED TO THE REFLECTION SET AT THE FINAL ROUND OF REFINEMENT. SEE TERWILLIGER AND ...Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF THE HEME. BAYESIAN WEIGHTING WAS APPLIED TO THE REFLECTION SET AT THE FINAL ROUND OF REFINEMENT. SEE TERWILLIGER AND BERENDZEN, ACTA CRYST. D52:743-748 (1996). THE SOLVENT MOLECULES 129 AND 139 CAN BE MODELED ONLY FOR ONE ALTERNATIVE PROTEIN CONFORMATION.
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 26 / Occupancy sum hydrogen: 1263 / Occupancy sum non hydrogen: 1426.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→8 Å
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Refine LS restraints |
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