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Yorodumi- PDB-3oga: 1.75 Angstrom resolution crystal structure of a putative NTP pyro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oga | ||||||
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Title | 1.75 Angstrom resolution crystal structure of a putative NTP pyrophosphohydrolase (yfaO) from Salmonella typhimurium LT2 | ||||||
Components | Nucleoside triphosphatase nudI | ||||||
Keywords | HYDROLASE / Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 / unknown function / putative NTP pyrophosphohydrolase / infectious diseases / structural genomics / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Function / homology | Function and homology information dCTP diphosphatase / dTTP diphosphatase activity / dCTP diphosphatase activity / nucleotide diphosphatase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 1.75 Angstrom resolution crystal structure of a putative NTP pyrophosphohydrolase (yfaO) from Salmonella typhimurium LT2 Authors: Halavaty, A.S. / Minasov, G. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oga.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oga.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 3oga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oga_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 3oga_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 3oga_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 3oga_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/3oga ftp://data.pdbj.org/pub/pdb/validation_reports/og/3oga | HTTPS FTP |
-Related structure data
Related structure data | 3n77S S: Starting model for refinement |
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Similar structure data | |
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: 19062.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: nudI, STM2295, yfaO / Plasmid: pMSCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Magic References: UniProt: Q8ZNF5, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Chemical | #3: Chemical | ChemComp-PO4 / #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: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 8 mg/mL protein in 10 mM Tris/HCl pH 8.3, 500 mM NaCl, 5 mM BME. Crystallization condition: The JCSG+ suite condition 56 (1 M di-Ammonium phosphate 0.1 M Sodium acetate pH 4.5), VAPOR ...Details: 8 mg/mL protein in 10 mM Tris/HCl pH 8.3, 500 mM NaCl, 5 mM BME. Crystallization condition: The JCSG+ suite condition 56 (1 M di-Ammonium phosphate 0.1 M Sodium acetate pH 4.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 23, 2010 / Details: Be-Lenses/Diamond Laue Mono |
Radiation | Monochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 38224 / Num. obs: 38224 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.34 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3.06 / Num. unique all: 1863 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N77 Resolution: 1.75→29.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.647 / SU ML: 0.069 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.104 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→29.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 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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