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- PDB-4mqb: Crystal structure of thymidylate kinase from Staphylococcus aureu... -

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Basic information

Entry
Database: PDB / ID: 4mqb
TitleCrystal structure of thymidylate kinase from Staphylococcus aureus in complex with 2-(N-morpholino)ethanesulfonic acid
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / thymidylate kinase / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors
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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 2-(N-morpholino)ethanesulfonic acid
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F.
History
DepositionSep 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)48,4135
Polymers47,8292
Non-polymers5843
Water5,927329
1


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

B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4135
Polymers47,8292
Non-polymers5843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2350 Å2
ΔGint-13 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.134, 90.457, 49.524
Angle α, β, γ (deg.)90.00, 101.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.170252, -0.216923, 0.961228), (-0.221788, -0.942005, -0.251868), (0.960117, -0.25607, 0.112267)15.65495, 19.04752, 30.60565

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Components

#1: Protein Thymidylate kinase / dTMP kinase


Mass: 23914.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M MgCl2, 0.1 M MMES buffer, 20% PEG6000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2013 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 57729 / Num. obs: 57729 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F4I

4f4i


Resolution: 1.55→25.62 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.097 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19845 2929 5.1 %RANDOM
Rwork0.14241 ---
obs0.14528 54773 99.71 %-
all-54773 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.89 Å2
2---1.35 Å20 Å2
3---1.11 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.55→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 26 329 3615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193443
X-RAY DIFFRACTIONr_bond_other_d0.0010.023325
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9814654
X-RAY DIFFRACTIONr_angle_other_deg0.9837657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4155426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7224.138174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8215607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9791530
X-RAY DIFFRACTIONr_chiral_restr0.1340.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3241.4711680
X-RAY DIFFRACTIONr_mcbond_other3.29417.461679
X-RAY DIFFRACTIONr_mcangle_it3.9012.2182114
X-RAY DIFFRACTIONr_mcangle_other3.9273.362120
X-RAY DIFFRACTIONr_scbond_it8.7742.2591763
X-RAY DIFFRACTIONr_scbond_other8.5362.2921769
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.3613.1542548
X-RAY DIFFRACTIONr_long_range_B_refined7.5684149
X-RAY DIFFRACTIONr_long_range_B_other7.5674150
X-RAY DIFFRACTIONr_rigid_bond_restr7.2233419
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded21.35853357
LS refinement shellResolution: 1.548→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 210 -
Rwork0.194 3970 -
obs--97.66 %
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)
10.920.64660.080.99460.66550.9316-0.03730.07190.0073-0.03090.03670.0752-0.00550.00210.00060.023-0.0088-0.00810.0107-0.00530.038810.4568-5.590716.0316
20.5013-0.3356-0.47752.44610.9710.9836-0.01780.0363-0.0456-0.1383-0.00940.2733-0.0476-0.03410.02720.0255-0.0047-0.01870.029-0.0030.0601-2.546.928324.9801
30.814-0.2748-0.37351.2130.48430.532-0.0483-0.08870.0142-0.02020.02680.01290.0260.0490.02150.0169-0.0016-0.00750.0306-0.00080.00887.59614.956429.4889
40.78190.1687-0.04240.5975-0.08810.7598-0.05140.0024-0.0115-0.03920.032-0.0545-0.00720.01870.01940.0107-0.00260.00060.02150.00220.007519.35474.375718.6133
51.8032.3128-0.30136.8511-1.56034.5283-0.0175-0.06870.0030.1288-0.0783-0.1365-0.10260.0890.09580.01720.002-0.01780.0121-0.00690.0222-0.261126.1058-0.1351
60.4445-0.1722-0.22390.68110.15220.24780.0420.037-0.0357-0.0216-0.03960.0136-0.0469-0.0342-0.00230.01650.0025-0.01470.0080.00660.0374-3.506321.0494-9.8007
70.8574-0.0077-0.33890.07460.22590.8413-0.061-0.0552-0.04350.02320.00240.01190.09610.04680.05850.02430.006-0.00720.01240.00630.02320.729915.6437-1.3294
85.55282.67060.40832.52810.71431.1974-0.1346-0.0027-0.2296-0.07010.032-0.1230.2087-0.03340.10260.0786-0.0030.03550.03430.00190.0282-10.70528.04553.4573
92.94171.0478-0.86981.6392-0.45491.84070.095-0.20380.20330.1679-0.02130.119-0.16240.027-0.07370.0402-0.00420.00010.0358-0.01490.0292-7.378926.75679.7837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 36
2X-RAY DIFFRACTION2A37 - 83
3X-RAY DIFFRACTION3A84 - 123
4X-RAY DIFFRACTION4A124 - 205
5X-RAY DIFFRACTION5B1 - 8
6X-RAY DIFFRACTION6B9 - 83
7X-RAY DIFFRACTION7B84 - 139
8X-RAY DIFFRACTION8B140 - 177
9X-RAY DIFFRACTION9B178 - 204

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