+Open data
-Basic information
Entry | Database: PDB / ID: 1jdo | ||||||
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Title | SPERM WHALE MYOGLOBIN (FERROUS, NITRIC OXIDE BOUND) | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / GLOBIN / HEME / OXYGEN STORAGE / NITRIC OXIDE | ||||||
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 / DIFFERENCE FOURIER / Resolution: 1.9 Å | ||||||
Authors | Brucker, E.A. / Phillips Jr., G.N. | ||||||
Citation | Journal: Proteins / Year: 1998 Title: Nitric oxide myoglobin: crystal structure and analysis of ligand geometry. Authors: Brucker, E.A. / Olson, J.S. / Ikeda-Saito, M. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jdo.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jdo.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jdo_validation.pdf.gz | 800 KB | Display | wwPDB validaton report |
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Full document | 1jdo_full_validation.pdf.gz | 801.6 KB | Display | |
Data in XML | 1jdo_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1jdo_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jdo ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jdo | HTTPS FTP |
-Related structure data
Related structure data | 1hjtC 2splS 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: 17399.180 Da / Num. of mol.: 1 / Mutation: INS(M0), L29F, D122N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-NO / |
#5: Water | ChemComp-HOH / |
Sequence details | THIS STRUCTURE HAS THREE DIFFERENCES RELATIVE TO THE NATIVE SPERM WHALE PROTEIN: AN INITIATOR ...THIS STRUCTURE HAS THREE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.37 % |
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Crystal grow | pH: 9 / Details: pH 9. |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 14, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 17289 / % possible obs: 99 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 5.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 2SPL Resolution: 1.9→5 Å / Num. parameters: 5667 / Num. restraintsaints: 5401 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1382.3 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→5 Å
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Refine LS restraints |
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