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- PDB-1tsl: L. CASEI THYMIDYLATE SYNTHASE WITH SPECIES SPECIFIC INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1tsl
TitleL. CASEI THYMIDYLATE SYNTHASE WITH SPECIES SPECIFIC INHIBITOR
ComponentsTHYMIDYLATE SYNTHASE
KeywordsMETHYLTRANSFERASE / SPECIES SPECIFICITY / STRUCTURE-BASED DRUG DESIGN / ANTIBIOTIC
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-A15 / PHOSPHATE ION / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.5 Å
AuthorsStout, T.J. / Stroud, R.M.
CitationJournal: Biochemistry / Year: 1999
Title: Structure-based design of inhibitors specific for bacterial thymidylate synthase.
Authors: Stout, T.J. / Tondi, D. / Rinaldi, M. / Barlocco, D. / Pecorari, P. / Santi, D.V. / Kuntz, I.D. / Stroud, R.M. / Shoichet, B.K. / Costi, M.P.
History
DepositionJun 12, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)37,1633
Polymers36,6301
Non-polymers5322
Water5,639313
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3256
Polymers73,2612
Non-polymers1,0644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area6920 Å2
ΔGint-43 kcal/mol
Surface area26070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.300, 78.300, 243.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein THYMIDYLATE SYNTHASE / TS / THYMIDYLATE SYNTHETASE


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 WHICH LACKS A / 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-A15 / 3'-3"-DICHLOROPHENOL-1,8-3H-BENZO[DE]ISOCHROMEN-1-ONE / A156


Mass: 437.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H14Cl2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.8
Details: 6 MG/ML PROTEIN, PH 7.4; 1% AMMONIUM SULFATE, 1 MM DTT, + 1 % SATURATED LIGAND-DMSO SOLUTION. HANGING DROP OVER 20 MM KPO4, PH 6.8 AND 1 MM DTT., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
210 %ammonium sulfate1drop
31 mMdithiothreitol1drop
420 mM1reservoirKPO4
51 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→48.6 Å / Num. obs: 9477 / % possible obs: 58.7 % / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.0812 / Rsym value: 0.0812 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.125 / % possible all: 24.7
Reflection
*PLUS
Num. all: 29742 / Num. measured all: 78644
Reflection shell
*PLUS
% possible obs: 24.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
MSCdata reduction
MSCdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 4TMS

4tms


Resolution: 2.5→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 937 10.5 %SHELLS
Rwork0.163 ---
obs0.163 8931 57.4 %-
Displacement parametersBiso mean: 23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 35 313 2941
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.08
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.381.5
X-RAY DIFFRACTIONx_mcangle_it2.32
X-RAY DIFFRACTIONx_scbond_it1.862
X-RAY DIFFRACTIONx_scangle_it2.782.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 48 10.8 %
Rwork0.222 395 -
obs--17.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3A156.PARAMA156.TOPO
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.08
LS refinement shell
*PLUS
Rfactor obs: 0.222

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