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- PDB-3bz0: Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUM... -

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Basic information

Entry
Database: PDB / ID: 3bz0
TitleLactobacillus Casei Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00
ComponentsThymidylate synthase
KeywordsTRANSFERASE / NUCLEOTIDE SYNTHASE / 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 / 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-C00 / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLeone, R. / Cancian, L. / Costi, M.P. / Ferrari, S. / Luciani, R. / Mangani, 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 17, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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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
Water64936
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 operation12_565x,x-y+1,-z+1/61
Buried area5900 Å2
ΔGint-17 kcal/mol
Surface area25490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.916, 77.916, 224.183
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-335-

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-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


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1mM EDTA, 20 mM Tris-HCl, dUMP, 100mM ammonium phopshate, 5% (v/v) PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.7→33.37 Å / Num. all: 10447 / Num. obs: 10443 / % possible obs: 88.6 % / Observed criterion σ(I): 1.7 / Redundancy: 4 % / Biso Wilson estimate: 56.53 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 4.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1502 / Rsym value: 0.439 / % possible all: 92.3

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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: 2.7→33.37 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.801 / SU B: 15.15 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32619 932 8.9 %RANDOM
Rwork0.22582 ---
obs0.2349 9511 88.6 %-
all-10443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error free: 0.475 Å
Refinement stepCycle: LAST / Resolution: 2.7→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 45 36 2602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212648
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.9593598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.065303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42523.835133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.32415427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7581512
X-RAY DIFFRACTIONr_chiral_restr0.1540.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022049
X-RAY DIFFRACTIONr_nbd_refined0.2840.21250
X-RAY DIFFRACTIONr_nbtor_refined0.3310.21700
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3290.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.29
X-RAY DIFFRACTIONr_mcbond_it0.861.51572
X-RAY DIFFRACTIONr_mcangle_it1.51822462
X-RAY DIFFRACTIONr_scbond_it1.93331265
X-RAY DIFFRACTIONr_scangle_it2.9554.51136
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 58 -
Rwork0.355 700 -
obs-700 85.47 %

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