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Yorodumi- PDB-1f63: CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E... -
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-Basic information
Entry | Database: PDB / ID: 1f63 | ||||||
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Title | CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10) | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / myoglobin / heme / triple mutant / 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 / Resolution: 1.8 Å | ||||||
Authors | Brunori, M. / Cutruzzola, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H. | ||||||
Citation | Journal: Biophys.J. / Year: 1999 Title: Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10). Authors: Brunori, M. / Cutruzzola, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H. #1: Journal: TRENDS BIOCHEM.SCI. / Year: 1999 Title: Does Picosecond Protein Dynamics Have a Survival Value? Authors: Brunori, M. / Cutruzzola, F. / Savino, C. / Travaglini-Allocatelli, C. / Vallone, B. / Gibson, Q.H. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The Role of Cavities in Protein Dynamics: Crystal Structure of a Photolytic Intermediate of a Mutant Myoglobin Authors: Brunori, M. / Vallone, B. / Cutruzzola, F. / Travaglini-Allocatelli, C. / Berendzen, J. / Chu, K. / 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 | 1f63.cif.gz | 47.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f63.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 1f63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f63_validation.pdf.gz | 477.8 KB | Display | wwPDB validaton report |
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Full document | 1f63_full_validation.pdf.gz | 481.3 KB | Display | |
Data in XML | 1f63_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1f63_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/1f63 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/1f63 | HTTPS FTP |
-Related 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: 17461.250 Da / Num. of mol.: 1 / Mutation: L29Y, H64Q, T67R 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: Water | ChemComp-HOH / |
Compound details | Triple Mb mutant designed to mimick the properties of Ascaris suum Hb. The amino acid in the heme ...Triple Mb mutant designed to mimick the properties of Ascaris suum Hb. The amino acid in the heme distal site do not allow ligand binding to the heme without movement of the mutated Y(B10) and Q(E7) |
-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: 61.35 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 2.7 M Ammonium sulphate, 20 mM Tris-Cl, 1 mM EDTA, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: vapor diffusionDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. all: 60982 / Num. obs: 19613 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.249 / Num. unique all: 1079 / % possible all: 89.3 |
Reflection shell | *PLUS % possible obs: 89.3 % |
-Processing
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Refinement | Resolution: 1.8→15 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: PROTIN
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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