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- PDB-3c06: Lactobacillus CASEI Thymidylate Synthase Ternary Complex With DUM... -

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Basic information

Entry
Database: PDB / ID: 3c06
TitleLactobacillus CASEI Thymidylate Synthase Ternary Complex With DUMP and the Phtalimidic Derivative 14C in Multiple Binding Modes-Mode 1
ComponentsThymidylate synthase
KeywordsTRANSFERASE / METHYLTRANSFERASE / STRUCTURE-BASED DRUG DESIGN / Nucleotide biosynthesis
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / 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
Chem-14C / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLeone, R. / Mangani, S. / Cancian, L. / Costi, M.P. / Luciani, R. / Ferrari, S.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening
Authors: Mangani, S. / Cancian, L. / Leone, R. / Pozzi, C. / Lazzari, S. / Luciani, R. / Ferrari, S. / Costi, M.P.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2113
Polymers36,6301
Non-polymers5812
Water72140
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4236
Polymers73,2612
Non-polymers1,1624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5840 Å2
ΔGint-25 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.573, 76.573, 212.931
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

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Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 36630.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Plasmid: PKPTSD / Production host: Escherichia coli (E. coli) / Strain (production host): CHI-2913 / References: UniProt: P00469, 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-14C / 2-(2-chloropyridin-4-yl)-4-methyl-1H-isoindole-1,3(2H)-dione


Mass: 272.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9ClN2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 4mg/mL LcTS, 1mM EDTA, 40mM dUMP, 20mM TRIS HCl, 100mM ammonium phosphate, 5% PEG 400 (v/v), 10-12% ligand solution in DMSO, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.6→38.29 Å / Num. all: 11884 / Num. obs: 11884 / % possible obs: 98.6 % / Observed criterion σ(I): 1.7 / Redundancy: 8.4 % / Biso Wilson estimate: 57.048 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 6.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 9 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1700 / Rsym value: 0.434 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCA

1lca


Resolution: 2.6→38.29 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.864 / SU B: 12.572 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.904 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29179 565 4.8 %RANDOM
Rwork0.21864 ---
obs0.22212 11312 100 %-
all-11884 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 39 40 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212608
X-RAY DIFFRACTIONr_angle_refined_deg2.1151.9583549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9535300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78223.876129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.76515414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8881511
X-RAY DIFFRACTIONr_chiral_restr0.1260.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022017
X-RAY DIFFRACTIONr_nbd_refined0.2580.21256
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.210
X-RAY DIFFRACTIONr_mcbond_it0.8561.51551
X-RAY DIFFRACTIONr_mcangle_it1.54322445
X-RAY DIFFRACTIONr_scbond_it1.99431247
X-RAY DIFFRACTIONr_scangle_it2.9034.51104
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 38 -
Rwork0.257 813 -
obs-813 100 %

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