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Yorodumi- PDB-6qo9: Crystal structure of ribonucleotide reductase NrdF from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qo9 | ||||||
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Title | Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis soaked with manganese ions | ||||||
Components | Ribonucleoside-diphosphate reductase subunit betaRibonucleotide reductase | ||||||
Keywords | OXIDOREDUCTASE / Metal binding / Oxidation reduction process / 2'-Deoxyribonucleotide metabolism / DNA replication | ||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.299 Å | ||||||
Authors | Grave, K. / Hogbom, M. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2019 Title: Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access. Authors: Grave, K. / Lambert, W. / Berggren, G. / Griese, J.J. / Bennett, M.D. / Logan, D.T. / Hogbom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qo9.cif.gz | 377.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qo9.ent.gz | 303 KB | Display | PDB format |
PDBx/mmJSON format | 6qo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/6qo9 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/6qo9 | HTTPS FTP |
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-Related structure data
Related structure data | 6qo5SC 6qo7C 6qo8C 6qobC C: citing same article (ref.) S: Starting model for refinement |
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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: 37055.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: nrdF, GBAA_1372 / Variant: pXO1-/pXO2- deficient / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 References: UniProt: Q81TB4, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-MN / #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: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 - 2.0 M ammonium sulphate, 0.1 M Bis-Tris methane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Dec 6, 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: 1.299→28.7602449565 Å / Num. obs: 155351 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.749 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Rrim(I) all: 0.057 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 15233 / CC1/2: 0.796 / Rpim(I) all: 0.338 / Rrim(I) all: 0.632 / % possible all: 97.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QO5 Resolution: 1.299→28.76 Å / SU ML: 0.0956969656831 / Cross valid method: FREE R-VALUE / σ(F): 1.353 / Phase error: 14.7212112245
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.981 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.299→28.76 Å
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Refine LS restraints |
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LS refinement shell |
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