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- PDB-6qo8: Crystal structure of ribonucleotide reductase NrdF from Bacillus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qo8 | ||||||
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Title | Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis anaerobically soaked with ferrous ions | ||||||
![]() | Ribonucleoside-diphosphate reductase subunit beta | ||||||
![]() | OXIDOREDUCTASE / Metal binding / Oxidation reduction process / 2'-Deoxyribonucleotide metabolism / DNA replication | ||||||
Function / homology | ![]() ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grave, K. / Hogbom, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 374.2 KB | Display | ![]() |
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PDB format | ![]() | 300.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.9 KB | Display | ![]() |
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Full document | ![]() | 454.4 KB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qo5SC ![]() 6qo7C ![]() 6qo9C ![]() 6qobC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: nrdF, GBAA_1372 / Variant: pXO1-/pXO2- deficient / Production host: ![]() ![]() References: UniProt: Q81TB4, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BTB / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.86 % |
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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: ![]() ![]() ![]() |
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: 1.319→45.903 Å / Num. obs: 147577 / % possible obs: 97.86 % / Redundancy: 3.2 % / Biso Wilson estimate: 12.7813381668 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.319→1.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 13178 / CC1/2: 0.817 / Rpim(I) all: 0.343 / Rrim(I) all: 0.559 / % possible all: 87.89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QO5 Resolution: 1.31921770161→45.9034025688 Å / SU ML: 0.108767294041 / Cross valid method: FREE R-VALUE / σ(F): 1.35846052973 / Phase error: 15.0212539842 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.2211682502 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31921770161→45.9034025688 Å
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Refine LS restraints |
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LS refinement shell |
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