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- PDB-1tsv: THYMIDYLATE SYNTHASE R179A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1tsv
TitleTHYMIDYLATE SYNTHASE R179A MUTANT
ComponentsTHYMIDYLATE SYNTHASE
KeywordsTRANSFERASE / 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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsFiner-Moore, J. / Stroud, R.M.
Citation
Journal: Protein Eng. / Year: 1996
Title: Contribution of a salt bridge to binding affinity and dUMP orientation to catalytic rate: mutation of a substrate-binding arginine in thymidylate synthase.
Authors: Finer-Moore, J.S. / Fauman, E.B. / Morse, R.J. / Santi, D.V. / Stroud, R.M.
#1: Journal: Faseb J. / Year: 1993
Title: Stereochemistry of a Multistep(Slash)Bipartite Methyl Transfer Reaction: Thymidylate Synthase
Authors: Stroud, R.M. / Finer-Moore, J.S.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei
Authors: Finer-Moore, J.S. / Fauman, E.B. / Foster, P.G. / Perry, K.M. / Santi, D.V. / Stroud, R.M.
#3: Journal: Science / Year: 1987
Title: Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design
Authors: Hardy, L.W. / Finer-Moore, J.S. / Montfort, W.R. / Jones, M.O. / Santi, D.V. / Stroud, R.M.
History
DepositionDec 5, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / software / struct_ref_seq_dif / 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 / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)36,8532
Polymers36,5441
Non-polymers3081
Water1,06359
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7054
Polymers73,0892
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area5460 Å2
ΔGint-22 kcal/mol
Surface area25980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.500, 78.500, 243.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. THE DIMER IS GENERATED BY A CRYSTALLOGRAPHIC TWO-FOLD, THE TRANSFORMATION MATRIX MUST BE APPLY TO FRACTIONAL COORDINATES. SYMMETRY1 1 -1.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 -0.50000

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Components

#1: Protein THYMIDYLATE SYNTHASE /


Mass: 36544.340 Da / Num. of mol.: 1 / Mutation: R179A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Description: PURCHASED FROM SIGMA / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-7 mg/mlprotein1drop
240 mMpotassium phosphate1drop
31 mMdithiothreitol1drop
40.5-2.0 %satammonium sulfate1drop
50.25 MdUMP1drop
6phosphate1reservoir
7dithiothreitol1reservoir
8EDTA1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 5, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10087 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Num. measured all: 22798 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-GENdata reduction
SAINTdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.9→7 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 8989 92 %
Refinement stepCycle: LAST / Resolution: 2.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 20 59 2665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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