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- PDB-2feo: Mutant R188M of The Cytidine Monophosphate Kinase from E. coli co... -

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Basic information

Entry
Database: PDB / ID: 2feo
TitleMutant R188M of The Cytidine Monophosphate Kinase from E. coli complexed with dCMP
ComponentsCytidylate kinase
KeywordsSIGNALING PROTEIN / TRANSFERASE / NUCLEOTIDE MONOPHOSPHATE KINASE
Function / homology
Function and homology information


(d)CMP kinase / (d)CMP kinase activity / 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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Cytidylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1563
Polymers24,7521
Non-polymers4032
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.949, 72.949, 76.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DC / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P / Comment: dCMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.949 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 31, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 5424 / % possible obs: 92.3 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 84.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.339 509 10 %RANDOM
Rwork0.259 ---
all0.259 5424 --
obs0.259 5090 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.416 Å20 Å20 Å2
2---7.416 Å20 Å2
3---14.831 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 25 42 1756
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.56

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