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- PDB-3bnz: Crystal structure of Thymidylate Synthase ternary complex with dU... -

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Basic information

Entry
Database: PDB / ID: 3bnz
TitleCrystal structure of Thymidylate Synthase ternary complex with dUMP and 8A inhibitor
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Thymidylate 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-C16 / PHOSPHATE ION / 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. / Cancian, L. / Luciani, R. / Ferrari, S. / Costi, M.P. / 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
DepositionDec 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: 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 / pdbx_struct_special_symmetry / 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)37,2964
Polymers36,6301
Non-polymers6653
Water1,31573
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5928
Polymers73,2612
Non-polymers1,3316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area6270 Å2
ΔGint-36 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.563, 76.563, 213.073
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-383-

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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Chemical ChemComp-C16 / 4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile


Mass: 262.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100mM (NH4)H2PO4/(NH4)2HPO4, 5% v/v PEG 400, 20mM Tris-HCl buffer 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: 2.6→48.468 Å / Num. all: 12116 / Num. obs: 11978 / Biso Wilson estimate: 59.33 Å2 / Rmerge(I) obs: 0.169 / Rsym value: 0.169
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.418 / Num. unique all: 1715 / Rsym value: 0.418

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LCA

1lca


Resolution: 2.6→36.04 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.833 / Cross valid method: THROUGHOUT / ESU R: 1.305 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32347 568 4.8 %RANDOM
Rwork0.21414 ---
obs0.21913 11341 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: 45.236 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 45 73 2683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212711
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.9593690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5295313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32523.897136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.85215432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6981512
X-RAY DIFFRACTIONr_chiral_restr0.1340.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022107
X-RAY DIFFRACTIONr_nbd_refined0.2880.21359
X-RAY DIFFRACTIONr_nbtor_refined0.3240.21748
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3230.213
X-RAY DIFFRACTIONr_mcbond_it0.8341.51570
X-RAY DIFFRACTIONr_mcangle_it1.54922539
X-RAY DIFFRACTIONr_scbond_it2.00231141
X-RAY DIFFRACTIONr_scangle_it3.084.51151
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 39 -
Rwork0.284 819 -
obs--100 %

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