+Open data
-Basic information
Entry | Database: PDB / ID: 2bnd | ||||||
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Title | The structure of E. coli UMP kinase in complex with UDP | ||||||
Components | URIDYLATE KINASE | ||||||
Keywords | TRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / PYRIMIDINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleotide biosynthetic process / UDP biosynthetic process / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Briozzo, P. / Evrin, C. / Meyer, P. / Assairi, L. / Joly, N. / Barzu, O. / Gilles, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structure of Escherichia Coli Ump Kinase Differs from that of Other Nucleoside Monophosphate Kinases and Sheds New Light on Enzyme Regulation. Authors: Briozzo, P. / Evrin, C. / Meyer, P. / Assairi, L. / Joly, N. / Barzu, O. / Gilles, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bnd.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bnd.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bnd_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2bnd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2bnd_validation.xml.gz | 23 KB | Display | |
Data in CIF | 2bnd_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bnd ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bnd | HTTPS FTP |
-Related structure data
Related structure data | 2bneC 2bnfSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26013.303 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P29464, UniProt: P0A7E9*PLUS, EC: 2.7.4.4 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-POP / | #5: Water | ChemComp-HOH / | Compound details | FUNCTION: CATALYSATOR OF THE PHOSPHORYLATION OF UMP TO UDP, WITH ATP AS PREFERRED DONOR ENGINEERED ...FUNCTION: CATALYSATO | |
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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: 2.17 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980459 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980459 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. obs: 12836 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.3 |
Reflection shell | Highest resolution: 2.6 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BNF Resolution: 2.6→22.5 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.8121 Å2 / ksol: 0.357708 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→22.5 Å
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Refine LS restraints |
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Xplor file |
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