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Yorodumi- PDB-3gwy: Crystal structure of putative CTP pyrophosphohydrolase from Bacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gwy | ||||||
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Title | Crystal structure of putative CTP pyrophosphohydrolase from Bacteroides fragilis | ||||||
Components | Putative CTP pyrophosphohydrolase | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Patskovsky, Y. / Romero, R. / Gilmore, M. / Do, J. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Ctp Pyrophosphohydrolase from Bacteroides fragilis Authors: Patskovsky, Y. / Romero, R. / Gilmore, M. / Do, J. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gwy.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gwy.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 3gwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/3gwy ftp://data.pdbj.org/pub/pdb/validation_reports/gw/3gwy | 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 16356.661 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF2916 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LBB1 #2: 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: 1.77 Å3/Da / Density % sol: 30.42 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 5 Details: 100mM Bis-Tris pH 5.0, 27% PEG 3350, 200mM Ammonium acetate, 10% Glycerol, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 19, 2009 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 16236 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 3.9 % / Biso Wilson estimate: 33.728 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 0.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.005 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.205 / 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: 41.399 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 891 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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