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- PDB-1cke: CMP KINASE FROM ESCHERICHIA COLI FREE ENZYME STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1cke
TitleCMP KINASE FROM ESCHERICHIA COLI FREE ENZYME STRUCTURE
ComponentsPROTEIN (CYTIDINE MONOPHOSPHATE KINASE)
KeywordsTRANSFERASE / NUCLEOTIDE MONOPHOSPHATE KINASE
Function / homology
Function and homology information


(d)CMP kinase / : / CMP kinase activity / dCMP kinase activity / pyrimidine nucleotide metabolic process / nucleobase-containing small molecule interconversion / guanosine tetraphosphate binding / response to X-ray / ATP binding / cytosol
Similarity search - Function
Cytidylate kinase / Cytidylate kinase domain / Cytidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.75 Å
AuthorsBriozzo, P. / Golinelli-Pimpaneau, B.
Citation
Journal: Structure / Year: 1998
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: Journal: J.Biol.Chem. / Year: 1996
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: Journal: J.Bacteriol. / Year: 1995
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
DepositionSep 24, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CYTIDINE MONOPHOSPHATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8442
Polymers24,7481
Non-polymers961
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.721, 82.721, 61.077
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein PROTEIN (CYTIDINE MONOPHOSPHATE KINASE) / E.C.2.7.4.14 TRANSFERASE / CK / MSSA


Mass: 24748.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6I0, UMP/CMP kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1reservoirpH7.4
2ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 7, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
SHARPphasing
X-PLOR3.84refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.75→7 Å / σ(F): 2
Details: SIDE CHAIN FROM RESIDUE ARG 173 WAS NOT WELL DEFINED IN THE DENSITY AND WAS MODELED BY STEREOCHEMISTRY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 -10 %RANDOM
Rwork0.205 ---
obs0.205 185661 --
Displacement parametersBiso mean: 33.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 5 156 1776
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.462
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.64
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.271
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.64
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.271

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