+Open data
-Basic information
Entry | Database: PDB / ID: 4a7x | ||||||
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Title | Crystal structure of uridylate kinase from Helicobacter pylori | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Chu, C.H. / Liu, M.H. / Chen, P.C. / Sun, Y.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structures of Helicobacter Pylori Uridylate Kinase: Insight Into Release of the Product Udp Authors: Chu, C.H. / Chen, P.C. / Liu, M.H. / Li, Y.C. / Hsiao, C.D. / Sun, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a7x.cif.gz | 545.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a7x.ent.gz | 456.2 KB | Display | PDB format |
PDBx/mmJSON format | 4a7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/4a7x ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a7x | HTTPS FTP |
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-Related structure data
Related structure data | 4a7wC 2bndS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26208.449 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SG13009 / References: UniProt: P56106, UMP kinase #2: Chemical | ChemComp-UDP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 56 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 62731 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BND Resolution: 2.49→96.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 24.649 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.309 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.522 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→96.4 Å
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Refine LS restraints |
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