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Yorodumi- PDB-4bmu: Crystal Structure of Ribonucleotide Reductase di-manganese(II) Nr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bmu | ||||||
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Title | Crystal Structure of Ribonucleotide Reductase di-manganese(II) NrdF from Bacillus cereus | ||||||
Components | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETARibonucleotide reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 CEREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hersleth, H.-P. / Tomter, A.B. / Hammerstad, M. / Rohr, A.K. / Andersson, K.K. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Crystal Structure of Bacillus Cereus Class Ib Ribonucleotide Reductase Di-Iron Nrdf in Complex with Nrdi. Authors: Hammerstad, M. / Hersleth, H. / Tomter, A.B. / Rohr, A.K. / Andersson, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bmu.cif.gz | 133.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bmu.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/4bmu ftp://data.pdbj.org/pub/pdb/validation_reports/bm/4bmu | HTTPS FTP |
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-Related structure data
Related structure data | 4bmoC 4bmpC 4bmqSC 4bmrC 4bmtC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 1 - 287 / Label seq-ID: 1 - 287
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-Components
#1: Protein | Mass: 37052.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q81G55, ribonucleoside-diphosphate reductase #2: Chemical | ChemComp-MN / #3: 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: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M MG-FORMATE, 20% (W/V) PEG 3350, 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.06 Å / Num. obs: 40394 / % possible obs: 90.4 % / Observed criterion σ(I): 6 / Redundancy: 2.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 92.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BMQ Resolution: 1.9→47.1 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.576 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.838 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.1 Å
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Refine LS restraints |
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