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- PDB-2tdm: STRUCTURE OF THYMIDYLATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 2tdm
TitleSTRUCTURE OF THYMIDYLATE SYNTHASE
ComponentsTHYMIDYLATE SYNTHASE
KeywordsMETHYLTRANSFERASE / TRANSFERASE
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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.55 Å
AuthorsFiner-Moore, J. / Stroud, R.M.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei.
Authors: Finer-Moore, J. / Fauman, E.B. / Foster, P.G. / Perry, K.M. / Santi, D.V. / Stroud, R.M.
#1: 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.
History
DepositionMar 28, 1997Processing site: BNL
SupersessionAug 20, 1997ID: 1TDM
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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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)36,9392
Polymers36,6301
Non-polymers3081
Water84747
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8774
Polymers73,2612
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area5880 Å2
ΔGint-28 kcal/mol
Surface area26050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.600, 78.600, 240.200
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


Mass: 36630.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria)
Description: STRAIN CHI-2913 LACKS A THYMIDYLATE SYNTHASE GENE
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.92 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMpotassium phosphate1reservoir
320 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1990
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 12591 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.156 / Net I/σ(I): 9.4
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.8 / Rsym value: 0.52 / % possible all: 65
Reflection
*PLUS
Num. measured all: 46338 / Rmerge(I) obs: 0.156
Reflection shell
*PLUS
% possible obs: 65 % / Rmerge(I) obs: 0.52

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Processing

Software
NameClassification
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
RefinementResolution: 2.55→7 Å / σ(F): 2
Details: THE SIDE CHAIN OF ARG 23 IS IN TWO HALF-OCCUPIED CONFORMATIONS IN THE CRYSTAL STRUCTURE.
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 9566 67 %
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.55→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 20 47 2660
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / 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_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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