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Yorodumi- PDB-1f65: CRYSTAL STRUCTURE OF OXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f65 | ||||||
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Title | CRYSTAL STRUCTURE OF OXY 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 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 / Resolution: 1.7 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 | 1f65.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f65.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 1f65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f65_validation.pdf.gz | 481.2 KB | Display | wwPDB validaton report |
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Full document | 1f65_full_validation.pdf.gz | 484.7 KB | Display | |
Data in XML | 1f65_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1f65_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/1f65 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/1f65 | 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 | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-OXY / | #5: Water | ChemComp-HOH / | Compound details | Triple Mb mutant designed to mimick the properties of Ascaris suum Hb. We observed a H-bonding ...Triple Mb mutant designed to mimick the properties of Ascaris suum Hb. We observed a H-bonding pattern to heme bound O2 which is virtually identical to the one found in A. suum Hb. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.68 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 2.7 M Ammonium sulphate, 20 mM Tris-Cl, 1mM EDTA reduced with sodium dithionate and subsequently derivatised with dioxigen, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8.7 / 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: 120 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: May 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: 1.7→14.8 Å / Num. all: 26633 / Num. obs: 26622 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.143 / Num. unique all: 2511 / % possible all: 90.7 |
Reflection shell | *PLUS % possible obs: 90.7 % |
-Processing
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Refinement | Resolution: 1.7→14.8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: PROTIN
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Refinement step | Cycle: LAST / Resolution: 1.7→14.8 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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