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Yorodumi- PDB-6f6k: R2-like ligand-binding oxidase V72L mutant with anaerobically rec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f6k | ||||||
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Title | R2-like ligand-binding oxidase V72L 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 / MOLECULAR REPLACEMENT / Resolution: 1.982 Å | ||||||
Authors | Griese, J.J. / Hogbom, M. | ||||||
Citation | Journal: J. Biol. Inorg. Chem. / Year: 2018 Title: Ether cross-link formation in the R2-like ligand-binding oxidase. Authors: Griese, J.J. / Branca, R.M.M. / Srinivas, V. / Hogbom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f6k.cif.gz | 225.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f6k.ent.gz | 182.8 KB | Display | PDB format |
PDBx/mmJSON format | 6f6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f6k_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 6f6k_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 6f6k_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 6f6k_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/6f6k ftp://data.pdbj.org/pub/pdb/validation_reports/f6/6f6k | HTTPS FTP |
-Related structure data
Related structure data | 6f6cC 6f6eC 6f6fC 6f6gC 6f6hC 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
#1: Protein | Mass: 36976.832 Da / Num. of mol.: 2 / Mutation: V72L 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 #2: Chemical | #3: Chemical | ChemComp-FE2 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.34 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 22.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 6.8, streak-seeded with crystals of wild-type protein PH range: 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 37786 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.16 / Net I/σ(I): 6.37 |
Reflection shell | Resolution: 1.98→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.142 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 5524 / CC1/2: 0.443 / Rrim(I) all: 1.365 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HR4 Resolution: 1.982→43.574 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.982→43.574 Å
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Refine LS restraints |
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LS refinement shell |
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