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Yorodumi- PDB-2pqv: Crystal structure of MutT/nudix family protein from Streptococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pqv | ||||||
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Title | Crystal structure of MutT/nudix family protein from Streptococcus pneumoniae | ||||||
Components | MutT/nudix family protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MutT/nudix family protein / Streptococcus pneumoniae / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å | ||||||
Authors | Chang, C. / Binkowski, T.A. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of MutT/nudix family protein from Streptococcus pneumoniae. Authors: Chang, C. / Binkowski, T.A. / Zhou, M. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pqv.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pqv.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/2pqv ftp://data.pdbj.org/pub/pdb/validation_reports/pq/2pqv | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17736.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0119 / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q97T37, UniProt: A0A0H2UMZ7*PLUS #2: Chemical | ChemComp-PO4 / | #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: 2.13 Å3/Da / Density % sol: 42.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 20% PEG3350, 0.2 M Ammonium chloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2005 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50 Å / Num. all: 37031 / Num. obs: 36665 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 19.772 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.68 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.85 / Num. unique all: 3365 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.63→47.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.339 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.109 / 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: 21.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→47.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.68 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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