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Yorodumi- PDB-2q16: Structure of the E. coli inosine triphosphate pyrophosphatase Rgd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q16 | ||||||
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Title | Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP | ||||||
Components | HAM1 protein homolog | ||||||
Keywords | HYDROLASE / ITP pyrophosphatase x-ray structure enzyme mechanism substrate | ||||||
Function / homology | Function and homology information XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding ...XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / magnesium ion binding / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Singer, A.U. / Lam, R. / Proudfoot, M. / Skarina, T. / Savchenko, A. / Yakunin, A.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli. Authors: Savchenko, A. / Proudfoot, M. / Skarina, T. / Singer, A. / Litvinova, O. / Sanishvili, R. / Brown, G. / Chirgadze, N. / Yakunin, A.F. | ||||||
History |
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Remark 999 | sequence These residues belong to a TEV cleavage site. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q16.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q16.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 2q16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q16_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2q16_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2q16_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 2q16_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/2q16 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/2q16 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23475.980 Da / Num. of mol.: 2 / Mutation: D69A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yggV / Plasmid: pET15-b-based p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RP References: UniProt: P52061, nucleoside-triphosphate diphosphatase |
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-Non-polymers , 5 types, 420 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: 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: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25% PEG 4K, 200 mM Ammonium Sulfate, 100 mM Sodium Acetate, 2% iso-Propanol, 20 mM Calcium Chloride, 10mM ITP, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2006 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→500 Å / Num. all: 36421 / Num. obs: 36385 / % possible obs: 99.96 % / Redundancy: 19.4 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 39.9 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 17.7 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2359 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→26.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.965 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 29.725 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→26.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 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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