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Yorodumi- PDB-3n39: Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n39 | ||||||
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Title | Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with NrdI | ||||||
Components |
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Keywords | OXIDOREDUCTASE / ribonucleotide reductase / four-helix bundle / dimanganese cluster / flavoprotein | ||||||
Function / homology | Function and homology information ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein modification process / FMN binding / manganese ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Boal, A.K. / Cotruvo Jr., J.A. / Stubbe, J. / Rosenzweig, A.C. | ||||||
Citation | Journal: Science / Year: 2010 Title: Structural basis for activation of class Ib ribonucleotide reductase. Authors: Boal, A.K. / Cotruvo, J.A. / Stubbe, J. / Rosenzweig, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n39.cif.gz | 337.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n39.ent.gz | 275.9 KB | Display | PDB format |
PDBx/mmJSON format | 3n39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/3n39 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/3n39 | HTTPS FTP |
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-Related structure data
Related structure data | 3n37SC 3n38C 3n3aC 3n3bC 1rljS 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: 36475.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2676, JW2651, nrdF, ygaD / Production host: Escherichia coli (E. coli) References: UniProt: P37146, ribonucleoside-diphosphate reductase #2: Protein | Mass: 17216.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nrdI, ygaO, b2674, JW2649 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A772 #3: Chemical | ChemComp-MN / #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: 2.29 Å3/Da / Density % sol: 46.29 % |
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Crystal grow | pH: 7.6 Details: 20% PEG 3000, 0.1 M HEPES pH 7.6, 0.1 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33.84 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N37 and 1RLJ Resolution: 2.5→33.84 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 23.547 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.341 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.8 Å2 / Biso mean: 58.999 Å2 / Biso min: 6.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→33.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.569 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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