+Open data
-Basic information
Entry | Database: PDB / ID: 4n82 | ||||||
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Title | X-ray crystal structure of Streptococcus sanguinis NrdIox | ||||||
Components | Ribonucleotide reductase | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / RIBONUCLEOTIDE REDUCTASE / OXIDATION-REDUCTION / FLAVIN MONONUCLEOTIDE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sanguinis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å | ||||||
Authors | Boal, A.K. / Rosenzweig, A.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. Authors: Makhlynets, O. / Boal, A.K. / Rhodes, D.V. / Kitten, T. / Rosenzweig, A.C. / Stubbe, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n82.cif.gz | 138.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n82.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 4n82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n82_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4n82_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4n82_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 4n82_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/4n82 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/4n82 | HTTPS FTP |
-Related structure data
Related structure data | 4n83C 1rljS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20069.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Strain: SK36 / Gene: nrdI, SSA_2263 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3CR20 #2: Chemical | #3: Chemical | #4: 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: 2.6 Å3/Da / Density % sol: 52.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG 4000, ammonium sulfate, pH 5.6, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. obs: 33395 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RLJ Resolution: 1.88→47.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.68 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 max: 74.85 Å2 / Biso mean: 33.6281 Å2 / Biso min: 16.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→47.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.884→1.933 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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