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Yorodumi- PDB-3n38: Ribonucleotide Reductase NrdF from Escherichia coli Soaked with F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n38 | ||||||
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Title | Ribonucleotide Reductase NrdF from Escherichia coli Soaked with Ferrous Ions | ||||||
Components | Ribonucleoside-diphosphate reductase 2 subunit betaRibonucleotide reductase | ||||||
Keywords | OXIDOREDUCTASE / ribonucleotide reductase / four-helix bundle / diferrous cluster | ||||||
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 / manganese ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 3n38.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n38.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 3n38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/3n38 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/3n38 | HTTPS FTP |
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-Related structure data
Related structure data | 3n37SC 3n39C 3n3aC 3n3bC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36475.070 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.96 % |
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Crystal grow | pH: 7.6 Details: 25% PEG 4000, 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: 1.03324 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03324 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→68.53 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N37 Resolution: 1.9→68.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.045 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.08 Å2 / Biso mean: 34.621 Å2 / Biso min: 17.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→68.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.954 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 20.8898 Å / Origin y: 26.7728 Å / Origin z: -10.8397 Å
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