+Open data
-Basic information
Entry | Database: PDB / ID: 5xkv | ||||||
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Title | structure of sperm whale myoglobin F138W | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / myoglobin | ||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Yuan, H. | ||||||
Citation | Journal: Dalton Trans / Year: 2017 Title: Rational design of artificial dye-decolorizing peroxidases using myoglobin by engineering Tyr/Trp in the heme center Authors: Li, L.L. / Yuan, H. / Liao, F. / He, B. / Gao, S.Q. / Wen, G.B. / Tan, X. / Lin, Y.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xkv.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xkv.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/5xkv ftp://data.pdbj.org/pub/pdb/validation_reports/xk/5xkv | HTTPS FTP |
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-Related structure data
Related structure data | 5xkwC 5hluS 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: 17273.986 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: F138W 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 |
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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: 2.2 Å3/Da / Density % sol: 44.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Dec 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 30559 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rsym value: 0.059 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.8 % / Num. unique obs: 1312 / Rsym value: 0.487 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HLU Resolution: 1.4→35.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.95 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.364 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→35.54 Å
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Refine LS restraints |
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