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- PDB-3e2i: Crystal structure of Thymidine Kinase from S. aureus -

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Basic information

Entry
Database: PDB / ID: 3e2i
TitleCrystal structure of Thymidine Kinase from S. aureus
ComponentsThymidine kinase
KeywordsTRANSFERASE / ZN-BINDING / ATP-binding / DNA synthesis / Kinase / Nucleotide-binding
Function / homology
Function and homology information


thymidine kinase / thymidine kinase activity / DNA biosynthetic process / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsLam, R. / Johns, K. / Battaile, K.P. / Romanov, V. / Lam, K. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal structure of Thymidine Kinase from S. aureus
Authors: Lam, R. / Johns, K. / Battaile, K.P. / Romanov, V. / Lam, K. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9033
Polymers24,7451
Non-polymers1582
Water1,04558
1
A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules

A: Thymidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,61012
Polymers98,9804
Non-polymers6308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area7300 Å2
ΔGint-20 kcal/mol
Surface area29300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.621, 71.621, 96.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

21A-247-

HOH

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Components

#1: Protein Thymidine kinase


Mass: 24745.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: tdk / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIPL / References: UniProt: Q0H0G9, thymidine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M succinic acid pH 7.0, 15% PEG3350, cryo-protected using 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.979331 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2007 / Details: Si(111) double-crystal monochromator
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979331 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 17226 / % possible obs: 99.7 % / Redundancy: 24.5 % / Rmerge(I) obs: 0.064 / Χ2: 1.687
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.01-2.0822.90.18316490.836197.9
2.08-2.1725.20.15716840.921100
2.17-2.2625.20.12316871.0251100
2.26-2.3825.20.10516951.1351100
2.38-2.5325.10.09317101.2851100
2.53-2.7325.10.08217021.5911100
2.73-324.90.0717161.7621100
3-3.4424.80.05917361.9721100
3.44-4.3324.50.04817622.4311100
4.33-5022.60.05318853.813199.3

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.0144.81144692733
ANO_10.43102.0144.81144680
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_18.83-44.8100122124
ISO_16.31-8.8300259135
ISO_15.17-6.3100353134
ISO_14.48-5.1700436138
ISO_14.01-4.4800491133
ISO_13.67-4.0100556142
ISO_13.4-3.6700604135
ISO_13.18-3.400667140
ISO_13-3.1800707134
ISO_12.84-300748143
ISO_12.71-2.8400792141
ISO_12.6-2.7100833132
ISO_12.5-2.600858141
ISO_12.41-2.500914130
ISO_12.32-2.4100942143
ISO_12.25-2.3200961140
ISO_12.18-2.25001007133
ISO_12.12-2.18001048139
ISO_12.07-2.12001075141
ISO_12.01-2.07001096135
ANO_18.83-44.810.25201220
ANO_16.31-8.830.27202590
ANO_15.17-6.310.27903530
ANO_14.48-5.170.31904360
ANO_14.01-4.480.32104910
ANO_13.67-4.010.34205560
ANO_13.4-3.670.35906040
ANO_13.18-3.40.37706670
ANO_13-3.180.3807070
ANO_12.84-30.38607480
ANO_12.71-2.840.4407920
ANO_12.6-2.710.44808330
ANO_12.5-2.60.48508580
ANO_12.41-2.50.5209140
ANO_12.32-2.410.55409420
ANO_12.25-2.320.59709610
ANO_12.18-2.250.648010070
ANO_12.12-2.180.67010480
ANO_12.07-2.120.715010750
ANO_12.01-2.070.81010950
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
146.0355.0783.726SE23.310.81
236.77557.0972.459SE24.910.8
346.32357.23816.471SE33.680.86
434.16156.8516.515SE24.660.5
518.52751.13913.257SE48.970.75
656.56664.916.367SE33.060.43
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 17202
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.86-10066.40.819506
5.38-6.8660.20.895503
4.67-5.3860.50.932510
4.21-4.6753.40.929506
3.9-4.21550.932506
3.66-3.957.20.938504
3.47-3.6659.20.923515
3.31-3.4758.50.916523
3.17-3.3155.10.921539
3.04-3.1758.20.918585
2.93-3.0462.70.918588
2.83-2.9356.20.916610
2.74-2.8353.60.912620
2.66-2.7458.30.907663
2.58-2.6658.40.897676
2.51-2.58590.892691
2.45-2.5160.20.895701
2.39-2.4557.10.896707
2.33-2.3959.10.886739
2.28-2.3359.90.892770
2.23-2.2863.30.907748
2.19-2.2363.30.888788
2.14-2.19590.887804
2.1-2.14630.891791
2.07-2.163.30.858853
2.01-2.0769.70.8151256

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.5.0043refinement
PDB_EXTRACT3.006data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.01→44.81 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.633 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 871 5.1 %RANDOM
Rwork0.202 ---
obs0.203 17194 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 40.04 Å2 / Biso mean: 17.265 Å2 / Biso min: 6.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.01→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 7 58 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221377
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9641858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9895177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16424.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3781510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211016
X-RAY DIFFRACTIONr_mcbond_it0.6811.5875
X-RAY DIFFRACTIONr_mcangle_it1.30921419
X-RAY DIFFRACTIONr_scbond_it2.2553502
X-RAY DIFFRACTIONr_scangle_it3.7014.5437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.014-2.0660.279550.2021176123299.919
2.066-2.1220.232730.211451218100
2.122-2.1840.192650.19411231188100
2.184-2.2510.27710.19110721143100
2.251-2.3240.211480.17910521100100
2.324-2.4060.202540.19310241078100
2.406-2.4960.234530.1979911044100
2.496-2.5980.295580.231941999100
2.598-2.7130.253450.234919964100
2.713-2.8450.306480.223888936100
2.845-2.9980.309470.226840887100
2.998-3.1790.266510.213788839100
3.179-3.3970.269370.215773810100
3.397-3.6680.188420.194696738100
3.668-4.0150.211290.181665694100
4.015-4.4840.14240.174600624100
4.484-5.170.254230.164551574100
5.17-6.310.208200.22468488100
6.31-8.8370.201160.20837739499.746
8.837-44.8110.286120.2623425895.349
Refinement TLS params.Method: refined / Origin x: 35.937 Å / Origin y: 13.481 Å / Origin z: 12.536 Å
111213212223313233
T0.1067 Å20.0002 Å2-0.0117 Å2-0.0441 Å2-0.0359 Å2--0.0789 Å2
L1.877 °2-0.2124 °2-0.0657 °2-0.7463 °2-0.2179 °2--1.8932 °2
S0.003 Å °-0.0797 Å °0.1575 Å °0.1532 Å °-0.0289 Å °-0.0553 Å °-0.3488 Å °-0.0403 Å °0.0258 Å °

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