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- PDB-3byx: Lactobacillus CASEI Thymidylate Synthase Ternary Complex with DUM... -

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Basic information

Entry
Database: PDB / ID: 3byx
TitleLactobacillus CASEI Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 in Multiple Binding Modes
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Structure Based Drug Design / Methyltransferase / Nucleotide biosynthesis
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm
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-C00 / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 16, 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)37,2683
Polymers36,6301
Non-polymers6382
Water2,216123
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5366
Polymers73,2612
Non-polymers1,2754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5910 Å2
ΔGint-24 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.012, 77.012, 213.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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 / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-C00 / 2-(4-hydroxybiphenyl-3-yl)-4-methyl-1H-isoindole-1,3(2H)-dione


Mass: 329.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H15NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1mM EDTA, 100mM ammonium phosphate, 5% (v/v) PEG 400, 20mM Tris-HCl, 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: Feb 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.4→48.74 Å / Num. all: 13142 / Num. obs: 13070 / % possible obs: 84.4 % / Observed criterion σ(I): 1.9 / Redundancy: 5.4 % / Biso Wilson estimate: 38.664 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.47 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1470 / Rsym value: 0.415 / % possible all: 85.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCA

1lca


Resolution: 2.4→48.74 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.428 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.713 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.283 641 4.9 %RANDOM
Rwork0.204 ---
all0.208 12429 --
obs0.208 12429 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.059 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.326 Å0.709 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 45 123 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212729
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.973717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3695311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04923.852135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.65615427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5651512
X-RAY DIFFRACTIONr_chiral_restr0.120.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022132
X-RAY DIFFRACTIONr_nbd_refined0.2340.21251
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21750
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.216
X-RAY DIFFRACTIONr_mcbond_it0.6591.51608
X-RAY DIFFRACTIONr_mcangle_it1.18622528
X-RAY DIFFRACTIONr_scbond_it1.50731337
X-RAY DIFFRACTIONr_scangle_it2.2264.51189
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 61 -
Rwork0.226 872 -
all-933 -
obs-872 100 %

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