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- PDB-7dp4: Crystal structure of wild type Brugia malayi thymidylate synthase... -

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Basic information

Entry
Database: PDB / ID: 7dp4
TitleCrystal structure of wild type 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 / dihydrofolate reductase activity / methylation / mitochondrion / cytosol
Similarity search - Function
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
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: 1.5 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)35,6768
Polymers34,5221
Non-polymers1,1537
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-8 kcal/mol
Surface area13500 Å2
Unit cell
Length a, b, c (Å)81.434, 81.434, 105.370
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: 34522.438 Da / Num. of mol.: 1
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 / Deoxyuridine monophosphate


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


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
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: MARMOSAIC 300 mm CCD / 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: 1.5→30 Å / Num. obs: 65291 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Net I/σ(I): 26.06
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.16 / Num. unique obs: 6480 / CC1/2: 0.718 / CC star: 0.914 / Rpim(I) all: 0.331 / Rrim(I) all: 0.597 / % 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: 1.5→25.855 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.213 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1914 3311 5.074 %
Rwork0.1767 61938 -
all0.178 --
obs-65249 99.5 %
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: 25.565 Å2
Baniso -1Baniso -2Baniso -3
1-0.233 Å20.117 Å20 Å2
2--0.233 Å2-0 Å2
3----0.757 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 73 283 2654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132507
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172283
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.6613399
X-RAY DIFFRACTIONr_angle_other_deg1.3421.595294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26221.678143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44115428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0751520
X-RAY DIFFRACTIONr_chiral_restr0.060.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022831
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02564
X-RAY DIFFRACTIONr_nbd_refined0.2260.2510
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22112
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21160
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.222
X-RAY DIFFRACTIONr_nbd_other0.1880.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.230
X-RAY DIFFRACTIONr_mcbond_it1.3842.5151182
X-RAY DIFFRACTIONr_mcbond_other1.3722.5111180
X-RAY DIFFRACTIONr_mcangle_it2.2553.7651484
X-RAY DIFFRACTIONr_mcangle_other2.2563.7651484
X-RAY DIFFRACTIONr_scbond_it1.822.7691325
X-RAY DIFFRACTIONr_scbond_other1.822.7711326
X-RAY DIFFRACTIONr_scangle_it2.8824.0431909
X-RAY DIFFRACTIONr_scangle_other2.8814.0461910
X-RAY DIFFRACTIONr_lrange_it5.20230.862984
X-RAY DIFFRACTIONr_lrange_other5.02330.1732905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5360.2942400.2614489X-RAY DIFFRACTION98.1935
1.536-1.5780.2762220.244439X-RAY DIFFRACTION99.9785
1.578-1.6240.2652260.2274318X-RAY DIFFRACTION100
1.624-1.6740.242450.224173X-RAY DIFFRACTION100
1.674-1.7280.2351980.2134090X-RAY DIFFRACTION100
1.728-1.7890.2322120.213914X-RAY DIFFRACTION100
1.789-1.8570.2221870.2043845X-RAY DIFFRACTION99.9504
1.857-1.9320.1992040.1913673X-RAY DIFFRACTION100
1.932-2.0180.2131640.1953516X-RAY DIFFRACTION99.8914
2.018-2.1170.2091850.1823361X-RAY DIFFRACTION99.9718
2.117-2.2310.1821790.1793204X-RAY DIFFRACTION99.9705
2.231-2.3660.1991670.1683024X-RAY DIFFRACTION99.8748
2.366-2.5290.1731480.172878X-RAY DIFFRACTION99.901
2.529-2.7320.2071630.172665X-RAY DIFFRACTION99.8235
2.732-2.9920.1691330.1692465X-RAY DIFFRACTION99.7313
2.992-3.3440.1831410.172211X-RAY DIFFRACTION99.7033
3.344-3.860.1651060.161987X-RAY DIFFRACTION99.1473
3.86-4.7240.16980.1331671X-RAY DIFFRACTION98.3324
4.724-6.6660.183590.1781331X-RAY DIFFRACTION97.8184
6.666-100.187340.187684X-RAY DIFFRACTION85.8852

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