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- PDB-1kdp: CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEO... -

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Basic information

Entry
Database: PDB / ID: 1kdp
TitleCYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-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 / 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: 2.3 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
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / reflns / reflns_shell / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value / _struct_site.details / _struct_site.pdbx_auth_comp_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)50,3636
Polymers49,5572
Non-polymers8074
Water6,215345
1
A: CYTIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1823
Polymers24,7781
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1823
Polymers24,7781
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.779, 75.981, 78.086
Angle α, β, γ (deg.)90, 90, 90
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
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: ESRF / Beamline: BM30A / Wavelength: 1.001 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 27, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 20232 / Num. obs: 19503 / % possible obs: 96.4 % / Observed criterion σ(I): 3 / Redundancy: 17 % / Rsym value: 0.045 / Net I/σ(I): 25.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 7.3 / Rsym value: 0.167 / % possible all: 95.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 20232 / Num. measured all: 345577 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 7.3

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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: 2.3→30 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 226, A 227, B 1, B 2, B 226, B 227) AND DISORDERED SIDE-CHAINS (A 27, A 111, A 152, B 23, B 30, B 161, B 210) WERE NOT INCLUDED IN MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1880 9.6 %RANDOM
Rwork0.219 ---
all-20232 --
obs-19521 96.5 %-
Displacement parametersBiso mean: 36.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 50 345 3791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_bond_d0.0096
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.4 Å2

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