+Open data
-Basic information
Entry | Database: PDB / ID: 1nqy | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of a CoA pyrophosphatase from D. Radiodurans | ||||||
Components | CoA pyrophosphatase (MutT/nudix family protein) | ||||||
Keywords | HYDROLASE / Nudix / pyrophosphatase / Dr1184 / CoA | ||||||
Function / homology | Function and homology information coenzyme A diphosphatase activity / coenzyme A catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.09 Å | ||||||
Authors | Kang, L.W. / Gabelli, S.B. / Bianchet, M.A. / Xu, W.L. / Bessman, M.J. / Amzel, L.M. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2003 Title: Structure of a coenzyme A pyrophosphatase from Deinococcus radiodurans: a member of the Nudix family. Authors: Kang, L.W. / Gabelli, S.B. / Bianchet, M.A. / Xu, W.L. / Bessman, M.J. / Amzel, L.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nqy.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nqy.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nqy_validation.pdf.gz | 364 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1nqy_full_validation.pdf.gz | 366.5 KB | Display | |
Data in XML | 1nqy_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 1nqy_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqy ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21273.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: Dr1184 / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RV46, nucleotide diphosphatase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.62 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG1500, MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.009 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→30 Å / Num. obs: 10529 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.061 / Net I/σ(I): 8.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 161533 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 94.3 % / Mean I/σ(I) obs: 8 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.09→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→30 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.295 / Rfactor Rwork: 0.248 |