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- PDB-1jut: E. coli Thymidylate Synthase Bound to dUMP and LY338529, A Pyrrol... -

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Basic information

Entry
Database: PDB / ID: 1jut
TitleE. coli Thymidylate Synthase Bound to dUMP and LY338529, A Pyrrolo(2,3-d)pyrimidine-based Antifolate
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / antifolate / dTMP synthesis / cancer / drug resistance
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol
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
Chem-LYD / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsSayre, P.H. / Finer-Moore, J.S. / Fritz, T.A. / Biermann, D. / Gates, S.B. / MacKellar, W.C. / Patel, V.F. / Stroud, R.M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases.
Authors: Sayre, P.H. / Finer-Moore, J.S. / Fritz, T.A. / Biermann, D. / Gates, S.B. / MacKellar, W.C. / Patel, V.F. / Stroud, R.M.
History
DepositionAug 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5316
Polymers61,1192
Non-polymers1,4114
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-14 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.800, 125.800, 67.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein THYMIDYLATE SYNTHASE / / TS


Mass: 30559.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: THYA / Plasmid: PTHYA-WT / Production host: Escherichia coli (E. coli) / Strain (production host): X2913 / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-LYD / 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-3-METHYL-BUTYRIC ACID / LY338529


Mass: 397.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N5O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: KPO4, MgCl2, DTT, EDTA, ammonium sulphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-10 mg/mlprotein1drop
230 %(w/v)PEG5000 MME1reservoir
30.1 Msodium cacodylate1reservoirpH6.5
40.2 Mammonium sulfate1reservoir
50.5 M1reservoirKCl

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 28, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 16866 / Num. obs: 16866 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 8
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 97881
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.599

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2KCE

2kce


Resolution: 2.7→29.59 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1797097.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1155 6.9 %RANDOM
Rwork0.218 ---
obs0.22 16719 99.5 %-
all-16719 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.6405 Å2 / ksol: 0.365014 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-1.4 Å20 Å2
2---0.67 Å20 Å2
3---1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 98 82 4486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.17
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 183 6.6 %
Rwork0.297 2571 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DUMP_LY338529.PARAMDUMP_LY338529.TOPO
X-RAY DIFFRACTION4FORM.PARAMFORM.TOPO
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 6.9 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor Rfree: 0.359 / % reflection Rfree: 6.6 % / Rfactor Rwork: 0.297

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