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- PDB-3gwc: Crystal structure of Mycobacterium tuberculosis thymidylate synth... -

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Basic information

Entry
Database: PDB / ID: 3gwc
TitleCrystal structure of Mycobacterium tuberculosis thymidylate synthase X bound to FdUMP and FAD
ComponentsThymidylate synthase thyX
KeywordsTRANSFERASE / ThyX / FAD / FdUMP / Flavoprotein / Methyltransferase / Nucleotide biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation
Similarity search - Function
Alpha-Beta Plaits - #3180 / Helix Hairpins - #440 / Helix Hairpins - #450 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Helix Hairpins / Helix non-globular / Special ...Alpha-Beta Plaits - #3180 / Helix Hairpins - #440 / Helix Hairpins - #450 / Thymidylate synthase ThyX / Thymidylate synthase ThyX superfamily / Thymidylate synthase complementing protein / Flavin-dependent thymidylate synthase (thyX) domain profile. / Helix Hairpins / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Flavin-dependent thymidylate synthase / Flavin-dependent thymidylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
E: Thymidylate synthase thyX
F: Thymidylate synthase thyX
G: Thymidylate synthase thyX
H: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,58125
Polymers229,5958
Non-polymers8,98617
Water16,880937
1
A: Thymidylate synthase thyX
B: Thymidylate synthase thyX
C: Thymidylate synthase thyX
D: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,33713
Polymers114,7984
Non-polymers4,5399
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24140 Å2
ΔGint-54 kcal/mol
Surface area33550 Å2
MethodPISA
2
E: Thymidylate synthase thyX
F: Thymidylate synthase thyX
G: Thymidylate synthase thyX
H: Thymidylate synthase thyX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,24512
Polymers114,7984
Non-polymers4,4478
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23620 Å2
ΔGint-54 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.044, 78.447, 168.959
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thymidylate synthase thyX / TS / TSase


Mass: 28699.430 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: thyX, Rv2754c, MT2824, MTV002.19c / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P66930, UniProt: P9WG57*PLUS, thymidylate synthase (FAD)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H12FN2O8P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 8000, 0.4 M KPO4, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97, 1.0
DetectorDetector: CCD / Date: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
211
ReflectionResolution: 1.9→50 Å / Num. obs: 151930 / % possible obs: 91.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.709 / % possible all: 82.6

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.512 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 7618 5 %RANDOM
Rwork0.187 ---
obs0.189 151875 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.04 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15077 0 598 937 16612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02116066
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210545
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.98822012
X-RAY DIFFRACTIONr_angle_other_deg1.037325482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77451935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36122.375720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.507152359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.53315163
X-RAY DIFFRACTIONr_chiral_restr0.2120.22481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117729
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023366
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_it0.7141.59745
X-RAY DIFFRACTIONr_mcbond_other0.1641.53845
X-RAY DIFFRACTIONr_mcangle_it1.29215680
X-RAY DIFFRACTIONr_scbond_it1.93636321
X-RAY DIFFRACTIONr_scangle_it3.0664.56332
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 476 -
Rwork0.277 9044 -
obs--78.26 %

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