[English] 日本語
Yorodumi- PDB-2feo: Mutant R188M of The Cytidine Monophosphate Kinase from E. coli co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2feo | ||||||
---|---|---|---|---|---|---|---|
Title | Mutant R188M of The Cytidine Monophosphate Kinase from E. coli complexed with dCMP | ||||||
Components | Cytidylate kinase | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / NUCLEOTIDE MONOPHOSPHATE KINASE | ||||||
Function / homology | Function and homology information (d)CMP kinase / cytidylate kinase activity / CMP kinase activity / dCMP kinase activity / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / guanosine tetraphosphate binding / response to X-ray / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ofiteru, A. / Bucurenci, N. / Alexov, E. / Bertrand, T. / Briozzo, P. / Munier-Lehmann, H. / Tourneux, L. / Barzu, O. / Gilles, A.M. | ||||||
Citation | Journal: Febs J. / Year: 2007 Title: Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase. Authors: Ofiteru, A. / Bucurenci, N. / Alexov, E. / Bertrand, T. / Briozzo, P. / Munier-Lehmann, H. / Gilles, A.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2feo.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2feo.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 2feo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/2feo ftp://data.pdbj.org/pub/pdb/validation_reports/fe/2feo | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 24752.336 Da / Num. of mol.: 1 / Mutation: R188M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: used helper phage M13K07 to perform the single mutation Gene: cmk, mssA / Plasmid: pHS210 / Production host: Escherichia coli (E. coli) / Strain (production host): CJ236 / References: UniProt: P0A6I0, UMP/CMP kinase |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-DC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: dCMP 200 mM, Tris-HCL 50 mM pH 7.4, ammonium sulfate 1.7 M, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 173 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.949 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 31, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.949 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. obs: 5424 / % possible obs: 92.3 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 84.6 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|