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Yorodumi- PDB-6f19: Structure of Mb NMH H64V, V68A mutant complex with EDA incubated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f19 | ||||||
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Title | Structure of Mb NMH H64V, V68A mutant complex with EDA incubated at room temperature for 5 min | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / Myoglobin / Heme / N-methylhistidine | ||||||
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: 1.895 Å | ||||||
Authors | Tinzl, M. / Hayashi, T. / Mori, T. / Hilvert, D. | ||||||
Citation | Journal: Nat Catal / Year: 2018 Title: Capture and characterization of a reactive haem-carbenoid complex in an artificial metalloenzyme Authors: Hayashi, T. / Tinzl, M. / Mori, T. / Krengel, U. / Proppe, J. / Soetbeer, J. / Klose, D. / Jeschke, G. / Reiher, M. / Hilvert, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f19.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f19.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 6f19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f19 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f19 | HTTPS FTP |
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-Related structure data
Related structure data | 6f17C 6f18C 6f1aC 6g5aC 6g5bC 6g5tC 1a6kS 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: 18210.963 Da / Num. of mol.: 1 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-EEE / |
#3: Chemical | ChemComp-HEM / |
#4: 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: 2.02 Å3/Da / Density % sol: 39.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M SPG buffer at pH 6.8-7.2 containing 28-32%(w/v) PEG1500. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.895→50 Å / Num. obs: 11935 / % possible obs: 97.6 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.895→2.01 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.5 / CC1/2: 0.934 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A6K Resolution: 1.895→40.65 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.895→40.65 Å
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Refine LS restraints |
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LS refinement shell |
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