[English] 日本語
Yorodumi- PDB-2cic: THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cic | ||||||
---|---|---|---|---|---|---|---|
Title | THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE WITH SUBSTRATE ANALOGUE DUPNHPP | ||||||
Components | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE | ||||||
Keywords | HYDROLASE / LIGAND COMPLEX / DRUG TARGET / DUTP PYROPHOSPHATASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CAMPYLOBACTER JEJUNI (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Moroz, O.V. / Harkiolaki, M. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine. Authors: Hemsworth, G.R. / Moroz, O.V. / Fogg, M.J. / Scott, B. / Bosch-Navarrete, C. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cic.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cic.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cic_validation.pdf.gz | 734.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2cic_full_validation.pdf.gz | 754.3 KB | Display | |
Data in XML | 2cic_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2cic_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2cic ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2cic | HTTPS FTP |
-Related structure data
Related structure data | 2cjeC 2yayC 2yazC 2yb0C 1w2yS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27051.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9PMK9, UniProt: Q0P8G4*PLUS | ||
---|---|---|---|
#2: Chemical | ChemComp-DUP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % |
---|---|
Crystal grow | Details: 3.5 M SODIUM FORMATE PH 7.0, 20 MM MAGNESIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 |
Detector | Date: Jul 21, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 33092 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.3 / % possible all: 90.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W2Y Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.698 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.21 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|