+Open data
-Basic information
Entry | Database: PDB / ID: 1a6n | ||||||
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Title | DEOXY-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 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: 1.15 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 | 1a6n.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6n.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a6n_validation.pdf.gz | 781.6 KB | Display | wwPDB validaton report |
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Full document | 1a6n_full_validation.pdf.gz | 787.1 KB | Display | |
Data in XML | 1a6n_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1a6n_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6n ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6n | HTTPS FTP |
-Related structure data
Related structure data | 1a6gC 1a6kC 1a6mC 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: 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: 35 % | ||||||||||||||||||||
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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: X12C / Wavelength: 0.91 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jan 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. obs: 45065 / % possible obs: 98 % / Observed criterion σ(I): -3 / Rsym value: 0.052 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.15→1.2 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.216 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 378009 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.216 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MBC Resolution: 1.15→8 Å / Num. parameters: 14248 / Num. restraintsaints: 48770 / 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. AQUOMET CONTAMINATION CORRECTED BY 30% OCCUPIED MODEL OF AQUOMET MYOGLOBIN. BAYESIAN DIFFERENCE REFINEMENT WAS USED ...Details: NO GEOMETRIC RESTRAINTS APPLIED TO IRON AND THE PLANAR ATOMS OF THE HEME. AQUOMET CONTAMINATION CORRECTED BY 30% OCCUPIED MODEL OF AQUOMET MYOGLOBIN. BAYESIAN DIFFERENCE REFINEMENT WAS USED AT THE FINAL STEP. SEE TERWILLIGER AND BERENDZEN, ACTA CRYST. D52:1004-1011 (1996). THE SOLVENT MOLECULES 81, 129, 139 AND 151 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: 1263.5 / Occupancy sum non hydrogen: 1424.1 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→8 Å
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Refine LS restraints |
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