+Open data
-Basic information
Entry | Database: PDB / ID: 1dti | ||||||
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Title | Recombinant sperm whale myoglobin h97d, d122n mutant (met) | ||||||
Components | PROTEIN (MYOGLOBIN) | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / HEME / OXYGEN TRANSPORT / MUSCLE PROTEIN / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.7 Å | ||||||
Authors | Liong, E.C. / Phillips Jr., G.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Waterproofing the heme pocket. Role of proximal amino acid side chains in preventing hemin loss from myoglobin. Authors: Liong, E.C. / Dou, Y. / Scott, E.E. / Olson, J.S. / 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 | 1dti.cif.gz | 47 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dti.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 1dti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dti_validation.pdf.gz | 811.2 KB | Display | wwPDB validaton report |
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Full document | 1dti_full_validation.pdf.gz | 815.3 KB | Display | |
Data in XML | 1dti_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1dti_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dti ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dti | HTTPS FTP |
-Related structure data
Related structure data | 1ch1C 1ch2C 1ch3C 1ch5C 1ch7C 1ch9C 1cikC 1cioC 1co8C 1co9C 1cp0C 1cp5C 1cpwC 1mbw 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: 17342.104 Da / Num. of mol.: 1 / Mutation: H97D, 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-HEM / |
#3: 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: 2.27 Å3/Da / Density % sol: 45.76 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.6-3.0 M (NH4)2SO4, 20 MM TRIS, 1 MM EDTA, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 9 / PH range high: 8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 24, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 17916 / % possible obs: 98 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044 |
Reflection | *PLUS Num. obs: 17917 / Num. measured all: 66693 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1MBW 1mbw Resolution: 1.7→5 Å / Num. parameters: 543 / Num. restraintsaints: 541 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1357 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→5 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.227 / Rfactor Rwork: 0.179 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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