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- PDB-7dp5: Crystal structure of mutant V45A Brugia malayi thymidylate syntha... -

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Basic information

Entry
Database: PDB / ID: 7dp5
TitleCrystal structure of mutant V45A Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate and methotrexate
ComponentsThymidylate synthase
KeywordsTRANSFERASE / THYMIDYLATE SYNTHASE / NUCLEOTIDE SYNTHASE / METHYLTRANSFERASE
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / mitochondrion / cytosol
Similarity search - Function
Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / METHOTREXATE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKeyunratsami, K. / Nualnoi, T. / Wongkamchai, S. / Songsiriritthigul, C. / Chen, C.-J. / Canyuk, B.
CitationJournal: To Be Published
Title: Crystallographic investigation and inhibition of Brugia malayi thymidylate synthase by a folate analog
Authors: Keyunratsami, K. / Nualnoi, T. / Wongkamchai, S. / Songsiriritthigul, C. / Chen, C.-J. / Canyuk, B.
History
DepositionDec 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5977
Polymers34,4941
Non-polymers1,1036
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-6 kcal/mol
Surface area13500 Å2
Unit cell
Length a, b, c (Å)81.281, 81.281, 105.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thymidylate synthase


Mass: 34494.387 Da / Num. of mol.: 1 / Mutation: V45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: Bma-tyms-1.1, BM_BM7277 / Plasmid: PQE-30 XA / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 [PREP4] / References: UniProt: A0A4E9EZW9, thymidylate synthase

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Non-polymers , 5 types, 259 molecules

#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 0.9 M sodium citrate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 12, 2013 / Details: DCM
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 53607 / % possible obs: 99.9 % / Redundancy: 4.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.023 / Rrim(I) all: 0.049 / Net I/σ(I): 34.73
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.61 / Num. unique obs: 5288 / CC1/2: 0.809 / CC star: 0.946 / Rpim(I) all: 0.259 / Rrim(I) all: 0.552

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HVY

1hvy


Resolution: 1.6→23.754 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.369 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1894 2722 5.082 %
Rwork0.1709 50843 -
all0.172 --
obs-53565 99.814 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.215 Å2
Baniso -1Baniso -2Baniso -3
1-0.129 Å20.065 Å2-0 Å2
2--0.129 Å20 Å2
3----0.419 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 73 253 2622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132471
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172252
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.663346
X-RAY DIFFRACTIONr_angle_other_deg1.3461.595226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53121.915141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47215425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9411519
X-RAY DIFFRACTIONr_chiral_restr0.0610.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
X-RAY DIFFRACTIONr_nbd_refined0.2290.2470
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22044
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21154
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2192
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2140.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.223
X-RAY DIFFRACTIONr_nbd_other0.2230.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.229
X-RAY DIFFRACTIONr_mcbond_it1.3092.1591164
X-RAY DIFFRACTIONr_mcbond_other1.3042.1551162
X-RAY DIFFRACTIONr_mcangle_it2.1573.2281455
X-RAY DIFFRACTIONr_mcangle_other2.1563.2281455
X-RAY DIFFRACTIONr_scbond_it1.7362.4321307
X-RAY DIFFRACTIONr_scbond_other1.7352.4341308
X-RAY DIFFRACTIONr_scangle_it2.7983.5451884
X-RAY DIFFRACTIONr_scangle_other2.7983.5471885
X-RAY DIFFRACTIONr_lrange_it5.11626.162854
X-RAY DIFFRACTIONr_lrange_other5.0325.6452797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6410.2481930.2413715X-RAY DIFFRACTION99.7957
1.641-1.6860.2512020.2263609X-RAY DIFFRACTION100
1.686-1.7340.2351950.2233533X-RAY DIFFRACTION100
1.734-1.7880.1971670.1973411X-RAY DIFFRACTION99.9721
1.788-1.8460.2361690.23378X-RAY DIFFRACTION99.9718
1.846-1.9110.2131850.1933175X-RAY DIFFRACTION99.9702
1.911-1.9830.221720.1923126X-RAY DIFFRACTION99.9697
1.983-2.0640.1861520.1793003X-RAY DIFFRACTION100
2.064-2.1560.211500.1782870X-RAY DIFFRACTION100
2.156-2.2610.2011490.1712773X-RAY DIFFRACTION100
2.261-2.3830.1551430.1552623X-RAY DIFFRACTION99.8917
2.383-2.5280.1711300.1632489X-RAY DIFFRACTION99.8856
2.528-2.7020.1761160.162357X-RAY DIFFRACTION99.9192
2.702-2.9180.1881110.1672193X-RAY DIFFRACTION99.9566
2.918-3.1960.1871120.172026X-RAY DIFFRACTION99.9533
3.196-3.5720.1951120.1591827X-RAY DIFFRACTION100
3.572-4.1230.165860.1421640X-RAY DIFFRACTION99.8265
4.123-5.0450.16890.1371381X-RAY DIFFRACTION99.8641
5.045-7.1170.194590.1761105X-RAY DIFFRACTION100
7.117-23.7540.172300.172609X-RAY DIFFRACTION91.6786

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