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- PDB-4fog: Crystal Structure of Mtb ThyA in Complex with 5-Fluoro-dUMP and 5... -

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Basic information

Entry
Database: PDB / ID: 4fog
TitleCrystal Structure of Mtb ThyA in Complex with 5-Fluoro-dUMP and 5-methyltetrahydrofolic acid
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / thymidylate synthase
Function / homology
Function and homology information


dUMP catabolic process / thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / response to antibiotic / cytosol / cytoplasm
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase ThyA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsReddy, M.C.M. / Bruning, J.B. / Harshbarger, W. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal structure of binary and ternary complexes of thymidylate synthase (ThyA) from Mycobacterium tuberculosis: Insights into the selectivity and mode of inhibition
Authors: Reddy, M.C.M. / Bruning, J.B. / Sacchettini, J.C.
History
DepositionJun 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,22211
Polymers119,5394
Non-polymers2,6837
Water5,368298
1
A: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3416
Polymers59,7702
Non-polymers1,5714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-16 kcal/mol
Surface area20110 Å2
MethodPISA
2
B: Thymidylate synthase
C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8815
Polymers59,7702
Non-polymers1,1123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-17 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.328, 82.317, 125.980
Angle α, β, γ (deg.)90.00, 132.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thymidylate synthase / / TS / TSase


Mass: 29884.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2834, MTV002.29c, Rv2764c, thyA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P67044, UniProt: P9WFR9*PLUS, thymidylate synthase
#2: Chemical
ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Fluorodeoxyuridylate


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12FN2O8P / Comment: inhibitor*YM
#3: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / Levomefolic acid


Mass: 459.456 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 298 K / pH: 6.4
Details: 2M ammonium sulfate, 0.1M imidazole pH 6.4, 5mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2009 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 5.16 % / Number: 278963 / Rmerge(I) obs: 0.097 / Χ2: 1 / D res high: 2.4 Å / D res low: 48.65 Å / Num. obs: 53664 / % possible obs: 98
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
5.1748.6598.80.050.785.12649
4.15.1799.10.0520.85.24290
3.584.198.80.080.935.09484
3.263.5898.40.1090.935.13270
3.023.2698.40.1711.015.21112
2.853.02980.2291.065.1958
2.72.8597.70.2931.095.1947
2.592.797.20.3861.185.09143
2.492.5997.20.3951.125.1622
2.42.4996.70.4461.145.1618
ReflectionResolution: 2.4→48.65 Å / Num. obs: 53664 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.16 % / Biso Wilson estimate: 44.17 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.16 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.9 / % possible all: 96.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.7 W8RSSIdata reduction
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QJ7

3qj7


Resolution: 2.4→42.94 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.38 / Isotropic thermal model: isotropic / σ(F): 0 / Phase error: 26.9 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.26 2712 5.07 %
Rwork0.211 --
obs0.214 53498 97.8 %
all-53498 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.66 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 42.32 Å2
Baniso -1Baniso -2Baniso -3
1--6.639 Å2-0 Å2-1.6528 Å2
2---0.6105 Å20 Å2
3---7.2496 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8272 0 183 298 8753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088778
X-RAY DIFFRACTIONf_angle_d1.14811998
X-RAY DIFFRACTIONf_dihedral_angle_d16.6423210
X-RAY DIFFRACTIONf_chiral_restr0.0751241
X-RAY DIFFRACTIONf_plane_restr0.0061522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44370.3051470.24952621X-RAY DIFFRACTION97
2.4437-2.49070.33361370.25922665X-RAY DIFFRACTION97
2.4907-2.54150.29881400.26642620X-RAY DIFFRACTION97
2.5415-2.59680.34811200.27062652X-RAY DIFFRACTION97
2.5968-2.65720.35131300.27822686X-RAY DIFFRACTION97
2.6572-2.72360.30161480.26252618X-RAY DIFFRACTION97
2.7236-2.79720.29921520.26422657X-RAY DIFFRACTION98
2.7972-2.87950.32551460.25422652X-RAY DIFFRACTION98
2.8795-2.97240.29811410.25372669X-RAY DIFFRACTION98
2.9724-3.07860.33581570.25292659X-RAY DIFFRACTION98
3.0786-3.20190.31451440.24322663X-RAY DIFFRACTION98
3.2019-3.34750.29951480.22962677X-RAY DIFFRACTION98
3.3475-3.52390.27381560.22412687X-RAY DIFFRACTION98
3.5239-3.74460.28331300.222713X-RAY DIFFRACTION98
3.7446-4.03350.2611300.20782696X-RAY DIFFRACTION99
4.0335-4.43910.22041490.16852715X-RAY DIFFRACTION99
4.4391-5.08050.18811510.1582715X-RAY DIFFRACTION99
5.0805-6.39760.20131350.1852736X-RAY DIFFRACTION99
6.3976-42.94580.21691510.17752685X-RAY DIFFRACTION95

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