[English] 日本語
Yorodumi- PDB-4lpi: A sperm whale myoglobin double mutant L29H/F43Y Mb with a distal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lpi | ||||||
---|---|---|---|---|---|---|---|
Title | A sperm whale myoglobin double mutant L29H/F43Y Mb with a distal hydrogen-bonding network | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Enzyme Function Initiative / distal heme hydrogen-bonding network / Nitrite redutase | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Lin, Y. | ||||||
Citation | Journal: Dalton Trans / Year: 2015 Title: How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin Authors: Yan, D.J. / Yuan, H. / Li, W. / Xiang, Y. / He, B. / Nie, C.M. / Wen, G.B. / Lin, Y.W. / Tan, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lpi.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lpi.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lpi_validation.pdf.gz | 812.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4lpi_full_validation.pdf.gz | 814.8 KB | Display | |
Data in XML | 4lpi_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 4lpi_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/4lpi ftp://data.pdbj.org/pub/pdb/validation_reports/lp/4lpi | HTTPS FTP |
-Related structure data
Related structure data | 5c6yC 4it8S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17407.137 Da / Num. of mol.: 1 / Mutation: L29H/F43Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.2 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate, 30% w/v Polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277KK |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→35.55 Å / Num. obs: 32680 / % possible obs: 7.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IT8 Resolution: 1.36→35.55 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8944 / SU ML: 0.3 / σ(F): 0.23 / Phase error: 17.13 / Stereochemistry target values: MLHL
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.459 Å2 / ksol: 0.397 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.56 Å2 / Biso mean: 15.3793 Å2 / Biso min: 5.09 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→35.55 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|