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- PDB-4f4i: Crystal structure of Thymidylate Kinase from Staphylococcus aureu... -

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Basic information

Entry
Database: PDB / ID: 4f4i
TitleCrystal structure of Thymidylate Kinase from Staphylococcus aureus in apo-form
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Midwest Center For Structural Genomics (Mcsg) / Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors (Mtbi) / Thymidylate Kinase
Function / homology
Function and homology information


dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate 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 speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. ...Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: Crystal structure of Thymidylate Kinase from Staphylococcus aureus in apo-form
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase


Theoretical massNumber of molelcules
Total (without water)52,3972
Polymers52,3972
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Thymidylate kinase

B: Thymidylate kinase


Theoretical massNumber of molelcules
Total (without water)52,3972
Polymers52,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1960 Å2
ΔGint-19 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.099, 91.022, 47.498
Angle α, β, γ (deg.)90.00, 104.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thymidylate kinase / / dTMP kinase


Mass: 26198.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: tmk, SAV0482 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: P65248, dTMP kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.84 Å3/Da / Density % sol: 33.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium Chloride, 0.1 M Hepes, 25 % PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2012 / Details: Beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.776
11L, -K, H20.224
ReflectionResolution: 2.5→30 Å / Num. all: 12948 / Num. obs: 12948 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4 / % possible all: 94.5

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4DWJ

4dwj


Resolution: 2.45→30 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.799 / SU B: 27.34 / SU ML: 0.272 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24162 605 4.7 %RANDOM
Rwork0.19423 ---
obs0.19643 12326 92.68 %-
all-12326 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20 Å235.09 Å2
2---19.23 Å20 Å2
3---16.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3122 0 0 40 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223185
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9724297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5175388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12924.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2415585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7911524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212396
X-RAY DIFFRACTIONr_mcbond_it0.4611.51940
X-RAY DIFFRACTIONr_mcangle_it0.84523144
X-RAY DIFFRACTIONr_scbond_it1.19831245
X-RAY DIFFRACTIONr_scangle_it2.0954.51153
LS refinement shellResolution: 2.455→2.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 4 -
Rwork0.23 72 -
obs--7.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.80142.5423-0.63125.91290.68652.46-0.04020.11420.2072-0.18930.01360.082-0.12320.01030.02660.12860.0332-0.05760.1707-0.02180.041211.5924-1.551115.5177
20.4133-0.3018-0.39880.36090.21320.4607-0.0025-0.00080.00940.0183-0.00190.0674-0.02340.00990.00440.1913-0.0118-0.05260.172-0.00060.13454.7836.105523.6885
31.29721.29950.83813.17421.38242.3762-0.0737-0.11310.13040.07170.0622-0.1066-0.14830.16250.01150.14860.03110.01440.2282-0.01570.180818.668715.243522.164
41.92191.0097-1.50445.0354-1.33233.9877-0.0924-0.087-0.1282-0.165-0.0065-0.1370.42070.13930.09890.13080.013-0.05540.1722-0.00130.131519.9136-5.336718.2844
53.03140.4374-0.67361.65450.15421.5599-0.2681-0.0443-0.0839-0.38840.1061-0.05850.0148-0.13550.1620.21410.0005-0.00550.19870.00310.0752-6.816223.76890.8215
60.4288-0.1224-0.05290.07260.07150.6419-0.01250.0205-0.02330.0003-0.05030.0779-0.03-0.02090.06270.1817-0.0006-0.01930.1903-0.00320.1767-1.389124.4219-9.6925
70.6488-0.0313-0.60370.4419-0.0680.5897-0.0014-0.0416-0.0196-0.0031-0.0190.03450.03960.0310.02050.22820.0057-0.00910.21060.0010.1203-1.402714.97530.3048
80.7402-0.2027-0.72641.97670.17080.7183-0.0297-0.1571-0.05620.1271-0.0429-0.01380.0540.12950.07270.2463-0.0031-0.04150.23110.00470.092-5.775919.09198.0264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION2A26 - 141
3X-RAY DIFFRACTION3A142 - 175
4X-RAY DIFFRACTION4A176 - 204
5X-RAY DIFFRACTION5B1 - 20
6X-RAY DIFFRACTION6B21 - 89
7X-RAY DIFFRACTION7B90 - 146
8X-RAY DIFFRACTION8B153 - 204

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