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Open data
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Basic information
Entry | Database: PDB / ID: 1cke | ||||||
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Title | CMP KINASE FROM ESCHERICHIA COLI FREE ENZYME STRUCTURE | ||||||
![]() | PROTEIN (CYTIDINE MONOPHOSPHATE KINASE) | ||||||
![]() | TRANSFERASE / NUCLEOTIDE MONOPHOSPHATE KINASE | ||||||
Function / homology | ![]() (d)CMP kinase / CMP kinase activity / dCMP kinase activity / (d)CMP 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Briozzo, P. / Golinelli-Pimpaneau, B. | ||||||
![]() | ![]() Title: Structures of escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity. Authors: Briozzo, P. / Golinelli-Pimpaneau, B. / Gilles, A.M. / Gaucher, J.F. / Burlacu-Miron, S. / Sakamoto, H. / Janin, J. / Barzu, O. #1: ![]() Title: Cmp Kinase from Escherichia Coli is Structurally Related to Other Nucleoside Monophosphate Kinases Authors: Bucurenci, N. / Sakamoto, H. / Briozzo, P. / Palibroda, N. / Serina, L. / Sarfati, R.S. / Labesse, G. / Briand, G. / Danchin, A. / Barzu, O. / Gilles, A.M. #2: ![]() Title: The Cmk Gene Encoding Cytidine Monophosphate Kinase is Located in the rspA Operon and is Required for Normal Replication Rate in Escherichia Coli Authors: Fricke, J. / Neuhard, J. / Kelln, R.A. / Pedersen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.1 KB | Display | ![]() |
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PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.8 KB | Display | ![]() |
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Full document | ![]() | 381.1 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 24748.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49 % | ||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 7, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 23804 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rsym value: 0.06 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.75→1.81 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.395 / % possible all: 99.6 |
Reflection | *PLUS Num. measured all: 185661 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.395 |
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Processing
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Refinement | Method to determine structure: ![]() Details: SIDE CHAIN FROM RESIDUE ARG 173 WAS NOT WELL DEFINED IN THE DENSITY AND WAS MODELED BY STEREOCHEMISTRY
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Displacement parameters | Biso mean: 33.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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