+Open data
-Basic information
Entry | Database: PDB / ID: 2bnf | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of E. coli UMP kinase in complex with UTP | ||||||
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 / phosphorylation / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bnf.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bnf.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 2bnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bnf ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bnf | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26562.018 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P29464, UniProt: P0A7E9*PLUS, EC: 2.7.4.4 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.45 % |
---|---|
Crystal grow | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.981019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981019 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→35 Å / Num. obs: 33118 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9 |
Reflection shell | Highest resolution: 2.45 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.45→35 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.9327 Å2 / ksol: 0.36074 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|