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- PDB-3qj7: Crystal Structure of the Mycobacterium tuberculosis Thymidylate s... -

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Basic information

Entry
Database: PDB / ID: 3qj7
TitleCrystal Structure of the Mycobacterium tuberculosis Thymidylate synthase (ThyA) bound to dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Thymidilate synthase / Structural Genomics / TB Structural Genomics Consortium / TBSGC
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
SPERMINE / 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: 2.504 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. / Harshbarger, W. / Sacchettini, J.C.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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)121,3239
Polymers119,8884
Non-polymers1,4355
Water9,998555
1
A: Thymidylate synthase
C: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7635
Polymers59,9442
Non-polymers8193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-29 kcal/mol
Surface area19830 Å2
MethodPISA
2
B: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5604
Polymers59,9442
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-27 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.956, 84.850, 130.065
Angle α, β, γ (deg.)90.000, 131.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-1567-

HOH

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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) / Gene: MT2834, MTV002.29c, 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-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% Peg 3k, 100mM Tris, 200mM NaCl, spermine additive, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97932 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2009 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 52086 / Num. obs: 52086 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 46.134 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Χ2: 2.404 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.5-2.543.70.3714.5326220.3711.59699.7
2.54-2.593.80.3315.1225520.3311.61599.6
2.59-2.643.80.2945.7925820.2941.63699.7
2.64-2.693.80.2666.9925640.2661.92599.9
2.69-2.753.80.2178.2426170.2171.80999.5
2.75-2.823.80.1949.5926120.1941.88199.7
2.82-2.893.90.1711.3425440.171.94899.5
2.89-2.963.90.14813.426170.1481.99499.7
2.96-3.053.90.12416.2425640.1242.13199.6
3.05-3.153.90.11319.2926210.1132.37100
3.15-3.263.90.09324.7625910.0932.53999.9
3.26-3.3940.0830.4326140.082.821100
3.39-3.553.90.07533.2525870.0753.00899.8
3.55-3.733.90.06838.3125990.0683.45599.9
3.73-3.973.90.06241.0426130.0623.13399.7
3.97-4.2740.05546.926200.0553.088100
4.27-4.74.10.0552.4426160.053.162100
4.7-5.384.10.04850.1526320.0482.824100
5.38-6.784.10.04451.0526450.0442.581100
6.78-503.90.03358.8426740.0332.18698.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BID

1bid


Resolution: 2.504→32.053 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8406 / SU ML: 0.35 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 2659 5.11 %random
Rwork0.1643 ---
obs0.167 52048 99.5 %-
all-52048 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.745 Å2 / ksol: 0.287 e/Å3
Displacement parametersBiso max: 118.57 Å2 / Biso mean: 44.6249 Å2 / Biso min: 14.85 Å2
Baniso -1Baniso -2Baniso -3
1--5.5471 Å2-0 Å2-3.1517 Å2
2---1.6195 Å20 Å2
3---7.1666 Å2
Refinement stepCycle: LAST / Resolution: 2.504→32.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8281 0 94 555 8930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078703
X-RAY DIFFRACTIONf_angle_d1.12811878
X-RAY DIFFRACTIONf_chiral_restr0.0741255
X-RAY DIFFRACTIONf_plane_restr0.0051521
X-RAY DIFFRACTIONf_dihedral_angle_d15.6733132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.504-2.54980.33551350.246624992634263495
2.5498-2.59880.36721250.2522257126962696100
2.5988-2.65180.31081500.2302257727272727100
2.6518-2.70950.28891320.2132257227042704100
2.7095-2.77250.28241700.1992257927492749100
2.7725-2.84180.28281640.1916255727212721100
2.8418-2.91850.26981380.1801260927472747100
2.9185-3.00440.2271220.172525792701270199
3.0044-3.10120.19331360.1724261427502750100
3.1012-3.2120.2581260.1638259727232723100
3.212-3.34050.21551430.1653263627792779100
3.3405-3.49230.20371220.1632261227342734100
3.4923-3.67620.23111390.1855259127302730100
3.6762-3.90620.22191320.167926102742274299
3.9062-4.20710.19541310.139262327542754100
4.2071-4.62940.16141390.1152263327722772100
4.6294-5.29670.1711460.1268261327592759100
5.2967-6.66340.18811490.1607265228012801100
6.6634-32.05530.20961600.1732266528252825100
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)
10.8040.10870.22340.3543-0.00880.18990.00930.05520.0201-0.0327-0.00740.01230.03380.023100.199-0.00230.00990.15640.00390.18853.45098.46035.8724
20.244-0.07550.22830.0348-0.07260.1810.02550.07010.0560.0101-0.02530.0574-0.0203-0.0533-00.2357-0.00940.03440.21550.05810.303546.211420.06362.7772
30.18070.0179-0.19990.4727-0.02650.61870.0067-0.0415-0.01830.0160.0367-0.0543-0.0072-0.035100.2086-0.0002-0.00450.23970.00960.17348.3898-2.051840.9259
40.08330.04290.16760.125-0.07350.10960.0307-0.255-0.1156-0.12270.17960.026-0.03560.0119-00.3099-0.040.03710.38660.02830.3099-3.6026-11.248844.2615
50.24080.11740.04520.1030.03910.31370.0848-0.1522-0.08430.1046-0.0638-0.0847-0.02710.0274-00.2339-0.008-0.04760.21910.04020.26873.79564.769825.2855
60.82410.05610.26750.25410.03450.40920.05910.0283-0.13230.0256-0.0284-0.10510.0291-0.0039-00.21660.0076-0.00030.20260.00290.263375.20443.329116.5918
70.05220.06440.02610.0478-0.08580.0660.05740.11690.1178-0.05540.04350.0364-0.0937-0.066900.3921-0.01920.02230.43160.02770.33230.86988.664316.0387
80.5216-0.0202-0.53770.3421-0.40490.92480.06140.09140.04320.0701-0.0503-0.0751-0.1393-0.001400.2026-0.009-0.01070.20440.0320.195317.711615.927523.6239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:206)A1 - 206
2X-RAY DIFFRACTION2(CHAIN A AND RESID 207:260)A207 - 260
3X-RAY DIFFRACTION3(CHAIN B AND RESID 1:222)B1 - 222
4X-RAY DIFFRACTION4(CHAIN B AND RESID 223:260)B223 - 260
5X-RAY DIFFRACTION5(CHAIN C AND RESID 1:83)C1 - 83
6X-RAY DIFFRACTION6(CHAIN C AND RESID 84:261)C84 - 261
7X-RAY DIFFRACTION7(CHAIN D AND RESID 0:24)D0 - 24
8X-RAY DIFFRACTION8(CHAIN D AND RESID 25:262)D25 - 262

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