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- PDB-4foa: Crystal Structure of the Mtb ThyA in Complex with 5-fluoro-dUMP -

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Basic information

Entry
Database: PDB / ID: 4foa
TitleCrystal Structure of the Mtb ThyA in Complex with 5-fluoro-dUMP
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 / cytoplasm / cytosol
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-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase ThyA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.253 Å
AuthorsReddy, M.C.M. / Bruning, J.B. / 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 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 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

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)121,1928
Polymers119,8884
Non-polymers1,3054
Water11,169620
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5964
Polymers59,9442
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-16 kcal/mol
Surface area20490 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5964
Polymers59,9442
Non-polymers6522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-15 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.796, 82.601, 125.584
Angle α, β, γ (deg.)90.00, 131.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thymidylate synthase / TS / TSase


Mass: 29971.908 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


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12FN2O8P / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M ammonium sulfate, 0.1 M imidazole 6.4, 5mM spermine, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97172 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2009 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97172 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 48.33 / Number: 294987 / Rmerge(I) obs: 0.051 / Χ2: 2.46 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 63595 / % possible obs: 96
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.15097.810.0332.2364.5
4.856.198.610.0352.5314.6
4.234.8595.910.0383.0324.5
3.854.2396.510.0433.334.6
3.573.8597.610.0483.3734.6
3.363.5797.410.0513.3344.6
3.193.3697.410.0563.1754.7
3.053.1997.310.0622.8744.7
2.943.0597.210.0712.7924.7
2.832.9496.910.0772.5714.7
2.752.8396.610.0852.5194.7
2.672.7596.410.0952.3094.7
2.62.6796.410.1042.1284.7
2.532.696.110.1152.0314.7
2.482.5395.810.1251.9734.7
2.422.4895.510.1431.8694.7
2.382.4295.510.1581.8054.7
2.332.3895.210.1661.7514.7
2.292.3395.210.191.7414.7
2.252.2985.110.2161.7084.4
ReflectionResolution: 2.25→50 Å / Num. all: 63595 / Num. obs: 63595 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 37.31 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Χ2: 2.461 / Net I/σ(I): 31.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.294.40.21628141.708185.1
2.29-2.334.70.1931491.741195.2
2.33-2.384.70.16631261.751195.2
2.38-2.424.70.15831311.805195.5
2.42-2.484.70.14331251.869195.5
2.48-2.534.70.12531541.973195.8
2.53-2.64.70.11531862.031196.1
2.6-2.674.70.10431812.128196.4
2.67-2.754.70.09531682.309196.4
2.75-2.834.70.08531982.519196.6
2.83-2.944.70.07732102.571196.9
2.94-3.054.70.07132032.792197.2
3.05-3.194.70.06231982.874197.3
3.19-3.364.70.05632343.175197.4
3.36-3.574.60.05132323.334197.4
3.57-3.854.60.04832363.373197.6
3.85-4.234.60.04331923.33196.5
4.23-4.854.50.03832123.032195.9
4.85-6.14.60.03532902.531198.6
6.1-504.50.03333562.236197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QJ7

3qj7


Resolution: 2.253→30.235 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.8518 / SU ML: 0.29 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 3234 5.09 %random
Rwork0.1643 ---
all0.1667 63581 --
obs0.1667 63581 96.43 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.569 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 163 Å2 / Biso mean: 41.7613 Å2 / Biso min: 14.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.3353 Å20 Å2-8.6785 Å2
2--0.1437 Å2-0 Å2
3---1.1916 Å2
Refinement stepCycle: LAST / Resolution: 2.253→30.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8285 0 80 620 8985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078721
X-RAY DIFFRACTIONf_angle_d1.05111927
X-RAY DIFFRACTIONf_chiral_restr0.0741273
X-RAY DIFFRACTIONf_plane_restr0.0051525
X-RAY DIFFRACTIONf_dihedral_angle_d13.9353184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.253-2.28650.24461270.19062506263392
2.2865-2.32220.27091350.19412575271095
2.3222-2.36030.29091410.19532559270095
2.3603-2.4010.25411530.19242566271995
2.401-2.44460.27561230.19392624274796
2.4446-2.49160.2461320.18712590272296
2.4916-2.54240.25061240.17542594271896
2.5424-2.59770.22211300.18162614274496
2.5977-2.65810.24791580.17822596275496
2.6581-2.72450.25361430.18852614275796
2.7245-2.79810.24741360.17552622275897
2.7981-2.88040.25321500.17732604275497
2.8804-2.97330.21731410.17592633277497
2.9733-3.07950.2411430.17692642278597
3.0795-3.20260.22271580.16992636279497
3.2026-3.34820.20251440.16782639278397
3.3482-3.52450.21841480.16172625277397
3.5245-3.74490.20361310.16462686281798
3.7449-4.03350.20551560.1542640279697
4.0335-4.43820.17021390.12922618275796
4.4382-5.07780.14131200.12222671279197
5.0778-6.38760.18721610.15282715287699
6.3876-30.23780.20291410.18752778291998
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)
11.52690.15320.02950.40670.55260.55270.1077-0.1596-0.04330.0844-0.0763-0.08990.08170.0307-0.05120.1984-0.00070.00680.07320.01490.1658-2.360510.878343.3501
21.13530.20850.19170.36950.12721.33330.04320.0031-0.13190.0258-0.06390.0840.032-0.17210.02020.1976-0.00180.02170.1717-0.00470.2336-24.60833.262128.4493
30.7711-0.164-0.04880.55010.15631.1973-0.00710.0361-0.115-0.0639-0.01810.0806-0.05280.16080.01970.1994-0.0096-0.01920.2332-0.00810.212542.5282-2.38347.8224
42.1581-0.0154-1.5380.7010.58552.51880.0794-0.52740.014-0.1773-0.13150.1693-0.47610.25410.04370.1938-0.0455-0.0390.2616-0.07430.150933.028516.506325.6872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:260)A0 - 260
2X-RAY DIFFRACTION2(chain B and resid 1:261)B1 - 261
3X-RAY DIFFRACTION3(chain C and resid 1:260)C1 - 260
4X-RAY DIFFRACTION4(chain D and resid 1:261)D1 - 261

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