+Open data
-Basic information
Entry | Database: PDB / ID: 5zzf | ||||||
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Title | X-ray structure of F43Y/H64D sperm whale myoglobin | ||||||
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: 1.6 Å | ||||||
Authors | Yuan, H. / Lin, Y.W. | ||||||
Citation | Journal: Acs Catalysis / Year: 2018 Title: A Rationally Designed Myoglobin Exhibits a Catalytic Dehalogenation Efficiency More than 1000-Fold That of a Native Dehaloperoxidase Authors: Yin, L.L. / Yuan, H. / Liu, C. / 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 | 5zzf.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zzf.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/5zzf ftp://data.pdbj.org/pub/pdb/validation_reports/zz/5zzf | HTTPS FTP |
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-Related structure data
Related structure data | 5zzgC 2jhoS 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: 17227.893 Da / Num. of mol.: 1 / Mutation: F43Y/H64D 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: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% w/v Polyethylene glycol 8000, 0.1 M Sodium cacodylate trihydrate pH 6.5, 0.2 M Sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 20810 / % possible obs: 99 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rsym value: 0.056 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3 / Num. unique obs: 1019 / Rpim(I) all: 0.183 / Rsym value: 0.39 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JHO Resolution: 1.6→31.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.559 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.911 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→31.01 Å
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