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- PDB-2ccg: Crystal structure of His-tagged S. aureus thymidylate kinase comp... -

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Basic information

Entry
Database: PDB / ID: 2ccg
TitleCrystal structure of His-tagged S. aureus thymidylate kinase complexed with thymidine monophosphate (TMP)
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / KINASE / NUCLEOTIDE BIOSYNTHESIS / TMP-BINDING / ATP-BINDING
Function / homology
Function and homology information


dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / ATP binding / cytosol
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate 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
THYMIDINE-5'-PHOSPHATE / Thymidylate kinase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKotaka, M. / Dhaliwal, B. / Ren, J. / Nichols, C.E. / Angell, R. / Lockyer, M. / Hawkins, A.R. / Stammers, D.K.
CitationJournal: Protein Sci. / Year: 2006
Title: Structures of S. Aureus Thymidylate Kinase Reveal an Atypical Active Site Configuration and an Intermediate Conformational State Upon Substrate Binding
Authors: Kotaka, M. / Dhaliwal, B. / Ren, J. / Nichols, C.E. / Angell, R. / Lockyer, M. / Hawkins, A.R. / Stammers, D.K.
History
DepositionJan 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,8964
Polymers51,2522
Non-polymers6442
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.540, 51.270, 72.940
Angle α, β, γ (deg.)90.00, 103.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.886, 0.05766, 0.46008), (0.05446, -0.99831, 0.02024), (0.46047, 0.00712, -0.88765)
Vector: -46.40665, 2.6442, 190.39627)

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Components

#1: Protein THYMIDYLATE KINASE / DTMP KINASE


Mass: 25625.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL HIS-TAGGED / Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CODON / References: UniProt: P65248, dTMP kinase
#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.1 Å3/Da / Density % sol: 40.83 %
Crystal growpH: 6.6
Details: 1M LICL, 0.1M NA CACODYLATE PH6.6, 18% PEG 6000, pH 6.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 12, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 15887 / % possible obs: 89.2 % / Observed criterion σ(I): -1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.1
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.6 / % possible all: 49

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4TMK AND 1GSI

4tmk

1gsi


Resolution: 2.3→29.16 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 775608.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.246 774 4.9 %RANDOM
Rwork0.2 ---
obs0.2 15856 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.1059 Å2 / ksol: 0.352492 e/Å3
Displacement parametersBiso mean: 63.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.08 Å20 Å28.53 Å2
2--3.58 Å20 Å2
3----9.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 42 100 3360
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.144
X-RAY DIFFRACTIONc_mcangle_it7.216
X-RAY DIFFRACTIONc_scbond_it8.626
X-RAY DIFFRACTIONc_scangle_it11.7610
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 84 4.9 %
Rwork0.297 1615 -
obs--58.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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