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- PDB-7dp6: Crystal structure of mutant V45T Brugia malayi thymidylate syntha... -

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Basic information

Entry
Database: PDB / ID: 7dp6
TitleCrystal structure of mutant V45T Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate
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; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)35,3578
Polymers34,5241
Non-polymers8337
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-9 kcal/mol
Surface area13630 Å2
Unit cell
Length a, b, c (Å)80.720, 80.720, 104.445
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Thymidylate synthase


Mass: 34524.414 Da / Num. of mol.: 1 / Mutation: V45T
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
#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-BME / BETA-MERCAPTOETHANOL


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl, 20 mM betamercaptoethanol, 8%(w/v) PEG 4000

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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 MX300-HS / 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: 1.85→30 Å / Num. obs: 34055 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.014 / Rrim(I) all: 0.031 / Net I/σ(I): 51.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.47 / Num. unique obs: 3402 / CC1/2: 0.876 / CC star: 0.966 / Rpim(I) all: 0.257 / Rrim(I) all: 0.56 / % possible all: 100

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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: 1.85→24.679 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.648 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.206 1723 5.067 %
Rwork0.1764 32284 -
all0.178 --
obs-34007 99.485 %
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: 40.835 Å2
Baniso -1Baniso -2Baniso -3
1-0.502 Å20.251 Å20 Å2
2--0.502 Å2-0 Å2
3----1.628 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 52 125 2462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172201
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.643246
X-RAY DIFFRACTIONr_angle_other_deg1.3311.5795103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5985290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29821.618136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78715411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3891519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
X-RAY DIFFRACTIONr_nbd_refined0.2160.2467
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.21980
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21139
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21025
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2620.2103
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.217
X-RAY DIFFRACTIONr_nbd_other0.2140.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1870.21
X-RAY DIFFRACTIONr_mcbond_it2.6714.0721148
X-RAY DIFFRACTIONr_mcbond_other2.674.0681147
X-RAY DIFFRACTIONr_mcangle_it3.666.0941436
X-RAY DIFFRACTIONr_mcangle_other3.6596.0981437
X-RAY DIFFRACTIONr_scbond_it3.8044.5651254
X-RAY DIFFRACTIONr_scbond_other3.8024.5681255
X-RAY DIFFRACTIONr_scangle_it5.8226.6331807
X-RAY DIFFRACTIONr_scangle_other5.8216.6361808
X-RAY DIFFRACTIONr_lrange_it7.9548.2062665
X-RAY DIFFRACTIONr_lrange_other7.948.1282655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.2751270.252361X-RAY DIFFRACTION99.6396
1.898-1.950.26980.2432314X-RAY DIFFRACTION99.7931
1.95-2.0060.2341230.2212260X-RAY DIFFRACTION99.9581
2.006-2.0680.2241260.2092178X-RAY DIFFRACTION99.9566
2.068-2.1360.2541150.2072103X-RAY DIFFRACTION99.9099
2.136-2.2110.2641010.2022055X-RAY DIFFRACTION100
2.211-2.2940.2041140.1911957X-RAY DIFFRACTION99.7111
2.294-2.3880.228980.1861914X-RAY DIFFRACTION100
2.388-2.4940.2081090.1851829X-RAY DIFFRACTION100
2.494-2.6150.227820.1711754X-RAY DIFFRACTION99.9456
2.615-2.7570.216940.181671X-RAY DIFFRACTION99.9434
2.757-2.9240.2791020.1911564X-RAY DIFFRACTION100
2.924-3.1250.211710.1791499X-RAY DIFFRACTION99.8093
3.125-3.3750.201840.1691389X-RAY DIFFRACTION99.8644
3.375-3.6960.179830.1551287X-RAY DIFFRACTION99.564
3.696-4.1310.149600.1471150X-RAY DIFFRACTION98.5342
4.131-4.7670.2490.1421031X-RAY DIFFRACTION97.561
4.767-5.8320.179420.171904X-RAY DIFFRACTION99.789
5.832-8.2190.206330.183704X-RAY DIFFRACTION99.1925
8.219-24.6790.195120.195358X-RAY DIFFRACTION81.6777

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