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Yorodumi- PDB-4bmo: Crystal Structure of Bacillus cereus Ribonucleotide Reductase di-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bmo | ||||||
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Title | Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex with NrdI (1.8 A resolution) | ||||||
Components |
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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 / protein modification process / FMN binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS CEREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Hammerstad, M. / Hersleth, H.-P. / 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 | 4bmo.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bmo.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/4bmo ftp://data.pdbj.org/pub/pdb/validation_reports/bm/4bmo | HTTPS FTP |
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-Related structure data
Related structure data | 4bmpC 4bmqC 4bmrC 4bmtC 4bmuC 2x2oS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37052.984 Da / Num. of mol.: 1 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 |
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#2: Protein | Mass: 13539.261 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B0YPL1 |
-Non-polymers , 4 types, 204 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-FMN / | #6: 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 6 Details: 2 M SODIUM CHLORIDE AND 0.1 M SODIUM CITRATE, PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→53.7 Å / Num. obs: 47107 / % possible obs: 98.2 % / Observed criterion σ(I): 6 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X2O Resolution: 1.81→53.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.774 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.112 / 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: 32.141 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→53.75 Å
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Refine LS restraints |
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