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- PDB-4e22: Structure of cytidine monophosphate kinase from Yersinia pseudotu... -

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Basic information

Entry
Database: PDB / ID: 4.0E+22
TitleStructure of cytidine monophosphate kinase from Yersinia pseudotuberculosis
ComponentsCytidylate kinase
KeywordsTRANSFERASE / P-loop / CMP/ATP binding
Function / homology
Function and homology information


(d)CMP kinase / (d)CMP kinase activity / pyrimidine nucleotide metabolic process / ATP binding / cytoplasm
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 speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.323 Å
AuthorsClark, E.A. / Acharya, K.R.
CitationJournal: Open Biol / Year: 2012
Title: Structure and function of cytidine monophosphate kinase from Yersinia pseudotuberculosis, essential for virulence but not for survival.
Authors: Walker, N.J. / Clark, E.A. / Ford, D.C. / Bullifent, H.L. / McAlister, E.V. / Duffield, M.L. / Acharya, K.R. / Oyston, P.C.
History
DepositionMar 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)27,8783
Polymers27,6861
Non-polymers1922
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.635, 88.635, 84.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Cytidylate kinase / CK / Cytidine monophosphate kinase / CMP kinase


Mass: 27685.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Strain: YPIII / Gene: cmk, YPK_2669 / Production host: Escherichia coli (E. coli) / References: UniProt: B1JRD8, (d)CMP kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 ul of 6 mg/ml Cmk (in 50 mM MES pH 6.0, 150 mM sodium chloride) plus 1 ul mother liquor (100 mM sodium HEPES pH 7.5, 1.2 M lithium sulfate, 100 mM magnesium chloride), VAPOR DIFFUSION, ...Details: 1 ul of 6 mg/ml Cmk (in 50 mM MES pH 6.0, 150 mM sodium chloride) plus 1 ul mother liquor (100 mM sodium HEPES pH 7.5, 1.2 M lithium sulfate, 100 mM magnesium chloride), VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2011
RadiationMonochromator: double crystal Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.32→27.43 Å / Num. obs: 10266 / Redundancy: 4.3 % / Biso Wilson estimate: 61.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.323→27.43 Å / SU ML: 0.55 / σ(F): 1.97 / Phase error: 30.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 495 4.83 %RANDOM
Rwork0.2218 ---
obs0.2245 10266 96.31 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.479 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1751 Å20 Å2-0 Å2
2--4.1751 Å20 Å2
3----8.3502 Å2
Refinement stepCycle: LAST / Resolution: 2.323→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 10 18 1655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081657
X-RAY DIFFRACTIONf_angle_d1.1682248
X-RAY DIFFRACTIONf_dihedral_angle_d16.998612
X-RAY DIFFRACTIONf_chiral_restr0.076266
X-RAY DIFFRACTIONf_plane_restr0.004295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.323-2.55640.3721210.29762334X-RAY DIFFRACTION92
2.5564-2.9260.32291180.2852544X-RAY DIFFRACTION100
2.926-3.6850.30541220.22932519X-RAY DIFFRACTION100
3.685-27.430.24391340.19412362X-RAY DIFFRACTION93

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