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Yorodumi- PDB-6f6b: R2-like ligand-binding oxidase A171F mutant with anaerobically re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f6b | ||||||
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Title | R2-like ligand-binding oxidase A171F mutant with anaerobically 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: 2.009 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 | 6f6b.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f6b.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 6f6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/6f6b ftp://data.pdbj.org/pub/pdb/validation_reports/f6/6f6b | HTTPS FTP |
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-Related structure data
Related structure data | 6f65C 6f6lC 6f6mC 4hr4S 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
#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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#2: Chemical | #3: Chemical | ChemComp-MN / | #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: 2.36 Å3/Da / Density % sol: 47.98 % |
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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: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.009→50 Å / Num. obs: 23799 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 44.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.088 / Net I/σ(I): 17.47 |
Reflection shell | Resolution: 2.009→2.13 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.668 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 3753 / CC1/2: 0.437 / Rrim(I) all: 1.811 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4HR4 Resolution: 2.009→48.618 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.009→48.618 Å
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Refine LS restraints |
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LS refinement shell |
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