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- PDB-2cmk: CYTIDINE MONOPHOSPHATE KINASE IN COMPLEX WITH CYTIDINE-DI-PHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 2cmk
TitleCYTIDINE MONOPHOSPHATE KINASE IN COMPLEX WITH CYTIDINE-DI-PHOSPHATE
ComponentsPROTEIN (CYTIDINE MONOPHOSPHATE KINASE)
KeywordsTRANSFERASE / 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
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
CYTIDINE-5'-DIPHOSPHATE / Cytidylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGolinelli-Pimpaneau, B. / Briozzo, P.
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.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 19, 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)25,3744
Polymers24,7781
Non-polymers5953
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.268, 77.268, 81.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 24778.334 Da / Num. of mol.: 1 / Fragment: DOMAIN
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.45 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMCDP1drop
30.4 Mammonium sulfate1drop
41.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975
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: 0.975 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 17252 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 16.6 % / Rsym value: 5 / Net I/σ(I): 25.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3 / Rsym value: 42.5 / % possible all: 95.9
Reflection
*PLUS
Num. measured all: 286435 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.425

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.84refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NON LIGATED CMPK

Resolution: 2→7 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.22 -5 %
Rwork0.213 --
obs0.213 16770 97.2 %
Displacement parametersBiso mean: 36.3 Å2
Refine analyzeLuzzati d res low obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 35 105 1839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.964
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.468
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
Highest resolution: 2 Å / Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.468

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