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

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Basic information

Entry
Database: PDB / ID: 4dwj
TitleCrystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / 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


dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / 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 subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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 complex with Thymidine Monophosphate
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Structure summary
Revision 1.2Oct 10, 2012Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase
C: Thymidylate kinase
D: Thymidylate kinase
E: Thymidylate kinase
F: Thymidylate kinase
G: Thymidylate kinase
H: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,84415
Polymers209,5888
Non-polymers2,2557
Water1,35175
1
A: Thymidylate kinase
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0414
Polymers52,3972
Non-polymers6442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-20 kcal/mol
Surface area19010 Å2
MethodPISA
2
C: Thymidylate kinase
D: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0414
Polymers52,3972
Non-polymers6442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-23 kcal/mol
Surface area18960 Å2
MethodPISA
3
E: Thymidylate kinase
G: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7193
Polymers52,3972
Non-polymers3221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-20 kcal/mol
Surface area18380 Å2
MethodPISA
4
F: Thymidylate kinase
H: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0414
Polymers52,3972
Non-polymers6442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-17 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.662, 73.409, 96.868
Angle α, β, γ (deg.)81.48, 90.10, 90.12
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999996, -0.002746, -0.000905), (-0.002753, -0.999966, -0.007742), (-0.000884, 0.007744, -0.99997)-0.08248, -102.79011, -16.7886

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Components

#1: Protein
Thymidylate kinase / dTMP kinase


Mass: 26198.518 Da / Num. of mol.: 8
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: Chemical
ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M MgCl2, 0.1 M HEPES, 25 % PEG3350, 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-D / Wavelength: 0.97886 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2011 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.74→30 Å / Num. all: 39979 / Num. obs: 39979 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 71.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.27
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2CCJ

2ccj


Resolution: 2.74→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 36.772 / SU ML: 0.347 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26817 2016 5 %RANDOM
Rwork0.20065 ---
obs0.20412 37963 94.71 %-
all-37963 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.257 Å2
Baniso -1Baniso -2Baniso -3
1-5.15 Å2-0.26 Å2-0.55 Å2
2---4.26 Å23.12 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.74→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12722 0 120 75 12917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913060
X-RAY DIFFRACTIONr_bond_other_d0.0030.028931
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.98117632
X-RAY DIFFRACTIONr_angle_other_deg1.108321750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.34151575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66124.349653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.399152378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.09215104
X-RAY DIFFRACTIONr_chiral_restr0.1010.21979
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214386
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022583
LS refinement shellResolution: 2.736→2.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 163 -
Rwork0.269 2747 -
obs--92.79 %
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)
10.7807-0.1352-0.48675.1092-0.8761.32810.04410.175-0.12-0.3912-0.0225-0.0955-0.0918-0.1257-0.02150.07260.0563-0.01790.2564-0.04070.163-1.2141-39.817-17.0285
21.0395-0.2661-0.52685.2354-0.20081.22750.19740.10280.056-0.0848-0.1095-0.537-0.24680.0142-0.08790.06230.02490.03030.23150.01740.2133.5849-25.2842-14.2611
30.47590.31760.27113.2868-0.85061.46930.0426-0.09960.08760.21480.00540.01060.0609-0.2879-0.0480.0309-0.00770.01240.2519-0.02590.1626-1.1932-62.889-0.2326
40.0445-0.2207-0.13854.23170.2915.19770.0421-0.046-0.00850.06570.0907-0.41860.26130.1707-0.13280.0692-0.0159-0.0330.19110.01850.23754.1135-77.6545-2.9188
50.86040.00130.09712.7307-0.6681.36510.10940.1681-0.0573-0.2458-0.0574-0.0439-0.0476-0.2698-0.0520.05530.05910.00190.2026-0.01530.1214-29.9693-83.5829-1.3147
61.1235-0.2532-0.42493.1022-0.00492.82840.04910.13340.10190.0064-0.034-0.2842-0.2119-0.2365-0.01510.06020.05750.01850.12750.03070.205-25.5613-69.08311.906
70.52970.1160.33525.0236-0.75810.89750.0458-0.14750.10230.4123-0.1703-0.18740.1317-0.0390.12450.0979-0.0570.01810.2556-0.05710.1688-30.337-33.901315.7321
81.1040.34110.35064.77720.05710.54980.2163-0.1312-0.04980.1005-0.2219-0.54810.15840.05750.00560.06250.0005-0.02310.22920.0380.2086-25.9367-49.107712.4266
91.41170.2297-0.33553.9388-0.90643.9406-0.00720.2452-0.2311-0.0790.09410.4230.0355-0.4313-0.08690.0228-0.0237-0.02560.179-0.02170.2-0.814-33.448530.9846
101.6486-0.34010.40674.37281.09998.4589-0.11680.1049-0.00520.13830.11220.0389-1.4245-0.18760.00460.30620.0040.04120.08390.01250.10063.536-17.987533.8278
111.6012-0.4163-0.05744.4099-1.53314.4174-0.0955-0.22970.2643-0.07410.42960.9136-0.0146-0.6616-0.3340.024-0.025-0.00980.265-0.00190.3406-33.562-41.0304-32.0139
121.94660.0581-0.29483.6574-0.56175.2081-0.0361-0.00940.1111-0.16730.19050.00760.6999-0.1199-0.15440.1005-0.0115-0.02820.11680.01790.1315-25.0002-49.5882-34.5405
130.7980.9380.49155.2611-1.67524.82190.2379-0.10470.21330.7994-0.15110.14840.48050.0081-0.08680.3902-0.06570.08620.0932-0.01580.16070.9469-56.579147.6884
141.12860.09830.29936.0074-0.12114.46990.40930.031-0.07050.5555-0.3097-0.70481.26370.4804-0.09960.72080.0775-0.09570.13450.0450.12977.5011-69.981445.2921
151.4705-0.0558-1.14554.4101-0.96644.29860.23120.2189-0.1147-0.8749-0.04270.4514-0.4614-0.2826-0.18850.45050.0961-0.11780.13020.01670.1473-30.932-75.413544.743
161.6317-0.3705-0.27946.88720.45194.17330.3534-0.02090.0033-0.7235-0.2971-0.6466-0.87030.3203-0.05630.4844-0.05630.07020.09850.04340.1359-22.3565-67.854549.3977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 123
2X-RAY DIFFRACTION2A124 - 204
3X-RAY DIFFRACTION3B2 - 125
4X-RAY DIFFRACTION4B126 - 204
5X-RAY DIFFRACTION5C2 - 134
6X-RAY DIFFRACTION6C135 - 204
7X-RAY DIFFRACTION7D2 - 126
8X-RAY DIFFRACTION8D127 - 204
9X-RAY DIFFRACTION9E2 - 128
10X-RAY DIFFRACTION10E129 - 204
11X-RAY DIFFRACTION11F2 - 81
12X-RAY DIFFRACTION12F82 - 204
13X-RAY DIFFRACTION13G2 - 122
14X-RAY DIFFRACTION14G123 - 203
15X-RAY DIFFRACTION15H1 - 82
16X-RAY DIFFRACTION16H83 - 203

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