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- PDB-3ik1: Lactobacillus casei Thymidylate Synthase in Ternary Complex with ... -

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Basic information

Entry
Database: PDB / ID: 3ik1
TitleLactobacillus casei Thymidylate Synthase in Ternary Complex with dUMP and the Phtalimidic Derivative 20C
ComponentsThymidylate synthase
KeywordsTRANSFERASE / nucleotide synthase / Methyltransferase / 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-20C / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPozzi, C. / Cancian, L. / Leone, R. / Luciani, R. / Ferrari, S. / Mangani, S. / Costi, M.P.
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
DepositionAug 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: 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)37,2363
Polymers36,6301
Non-polymers6052
Water2,864159
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4726
Polymers73,2612
Non-polymers1,2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area5980 Å2
ΔGint-19 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.985, 77.985, 224.718
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-321-

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) / Production host: Escherichia coli (E. coli) / References: UniProt: P00469, thymidylate synthase
#2: Chemical ChemComp-20C / 2-hydroxy-4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzoic acid / 2-hydroxy-4-(4-methyl-1,3-dioxo-2,3-dihydro-1H- isoindol-2-yl)benzoic acid


Mass: 297.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11NO5
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 10% saturated Ammonium sulfate, 1mM DTT, 20mM Potassium phosphate , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.983 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2008
RadiationMonochromator: Silicon (111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2.25→74.95 Å / Num. obs: 20159 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 19.9 % / Biso Wilson estimate: 33.669 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 37.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 20.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 10.8 / Num. unique all: 2868 / Rsym value: 0.286 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TDM

2tdm


Resolution: 2.25→67.54 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.201 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.285 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27083 1024 5.1 %RANDOM
Rwork0.21164 ---
obs0.21457 19048 99.85 %-
all-20103 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.236 Å0.285 Å
Refinement stepCycle: LAST / Resolution: 2.25→67.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 42 159 2762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212689
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.9583659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6775310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50123.897136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.80915431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5651512
X-RAY DIFFRACTIONr_chiral_restr0.1360.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212096
X-RAY DIFFRACTIONr_mcbond_it1.1231.51554
X-RAY DIFFRACTIONr_mcangle_it2.07622512
X-RAY DIFFRACTIONr_scbond_it2.85831135
X-RAY DIFFRACTIONr_scangle_it4.364.51147
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 89 -
Rwork0.264 1353 -
obs-1353 99.93 %

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