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- PDB-1kdr: CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH ARA-CYT... -

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Basic information

Entry
Database: PDB / ID: 1kdr
TitleCYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH ARA-CYTIDINE MONOPHOSPHATE
ComponentsCYTIDYLATE 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTOSINE ARABINOSE-5'-PHOSPHATE / Cytidylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBertrand, T. / Briozzo, P. / Assairi, L. / Ofiteru, A. / Bucurenci, N. / Munier-Lehmann, H. / Golinelli-Pimpaneau, B. / Barzu, O. / Gilles, A.M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme.
Authors: Bertrand, T. / Briozzo, P. / Assairi, L. / Ofiteru, A. / Bucurenci, N. / Munier-Lehmann, H. / Golinelli-Pimpaneau, B. / Barzu, O. / Gilles, A.M.
History
DepositionNov 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: CYTIDYLATE KINASE
B: CYTIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4917
Polymers49,5572
Non-polymers9355
Water1,44180
1
A: CYTIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1983
Polymers24,7781
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2944
Polymers24,7781
Non-polymers5153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.585, 73.772, 77.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein CYTIDYLATE KINASE / E.C.2.7.4.14 / Cytidine Monophosphate Kinase / CK / CMP KINASE


Mass: 24778.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cmk / Plasmid: pHSP210 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6I0, UMP/CMP kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CAR / CYTOSINE ARABINOSE-5'-PHOSPHATE


Type: RNA linking / Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.4 Mammonium sulfate1reservoir
250 mMTris-HCl1reservoirpH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.968 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.25→15 Å / Num. all: 19192 / Num. obs: 17963 / % possible obs: 93.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.2 % / Rsym value: 8.3 / Net I/σ(I): 14
Reflection shellResolution: 2.25→2.33 Å / Mean I/σ(I) obs: 4.25 / Rsym value: 27.4 / % possible all: 94.9
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 19192 / Num. measured all: 196124 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 94.9 % / Rmerge(I) obs: 0.274

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CMK

2cmk


Resolution: 2.25→15 Å / Isotropic thermal model: OVERALL ANISOTROPIC B / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: DISORDERED RESIDUES (A 1, A 2, A 224, A 225, A 226, A 227, B 1, B 2, B 224, B 225, B 226, B 227) WERE NOT INCLUDED IN MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1698 10 %RANDOM
Rwork0.199 ---
all-19192 --
obs-16923 81.9 %-
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 2.25→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3398 0 57 80 3535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_bond_d0.0054
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.3 Å2

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