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Yorodumi- PDB-6f65: R2-like ligand-binding oxidase A171F mutant with aerobically reco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f65 | ||||||
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Title | R2-like ligand-binding oxidase A171F mutant with aerobically reconstituted Mn/Fe cofactor | ||||||
Components | Ribonucleotide reductase small subunit | ||||||
Keywords | OXIDOREDUCTASE / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.948 Å | ||||||
Authors | Griese, J.J. / Hogbom, M. | ||||||
Citation | Journal: J. Biol. Inorg. Chem. / Year: 2019 Title: Assembly of a heterodinuclear Mn/Fe cofactor is coupled to tyrosine-valine ether cross-link formation in the R2-like ligand-binding oxidase. Authors: Griese, J.J. / Kositzki, R. / Haumann, M. / Hogbom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f65.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f65.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 6f65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f65_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 6f65_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 6f65_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6f65_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/6f65 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/6f65 | HTTPS FTP |
-Related structure data
Related structure data | 6f6bC 6f6lC 6f6mC 4hr0S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37038.902 Da / Num. of mol.: 1 / Mutation: A171F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria) Strain: HTA426 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase |
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-Non-polymers , 5 types, 64 molecules
#2: Chemical | ChemComp-FE / |
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#3: Chemical | ChemComp-MN3 / |
#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-OCA / |
#6: 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: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.5 / PH range: 7.5 |
-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 PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.948→50 Å / Num. obs: 25690 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 43.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.052 / Net I/σ(I): 15.33 |
Reflection shell | Resolution: 1.948→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 4075 / CC1/2: 0.604 / Rrim(I) all: 1.034 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4HR0 Resolution: 1.948→48.5 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.81 / 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: 1.948→48.5 Å
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Refine LS restraints |
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LS refinement shell |
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