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- PDB-2fem: Mutant R188M of the Cytidine Monophosphate Kinase From E. Coli -

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Basic information

Entry
Database: PDB / ID: 2fem
TitleMutant R188M of the Cytidine Monophosphate Kinase From E. Coli
ComponentsCytidylate kinase
KeywordsSIGNALING PROTEIN / TRANSFERASE / NUCLEOTIDE MONOPHOSPHATE KINASE
Function / homology
Function and homology information


(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
Cytidylate kinase / Cytidylate kinase domain / Cytidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOfiteru, A. / Bucurenci, N. / Alexov, E. / Bertrand, T. / Briozzo, P. / Munier-Lehmann, H. / Tourneux, L. / Barzu, O. / Gilles, A.M.
CitationJournal: 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
DepositionDec 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytidylate kinase


Theoretical massNumber of molelcules
Total (without water)24,7521
Polymers24,7521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.167, 82.167, 60.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a monomer

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Components

#1: Protein Cytidylate kinase / E.C.2.7.4.14 / Cytidine monophosphate kinase / CK / CMP kinase / Protein mssA / p25


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

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Tris-HCL 50 mM pH 7.4, ammonium sulfate 1.3 M, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 14, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 18504 / Num. obs: 18054 / % possible obs: 97.9 % / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→2 Å / % possible all: 86.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1770 10.5 %RANDOM
Rwork0.2309 ---
all0.231 18504 --
obs0.231 18054 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-3.149 Å20 Å2
2---0.8 Å20 Å2
3---1.601 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 0 0 1614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.27

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