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- PDB-2tsr: THYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX -

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Basic information

Entry
Database: PDB / ID: 2tsr
TitleTHYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX
ComponentsTHYMIDYLATE SYNTHASE
KeywordsMETHYLTRANSFERASE / THYMIDYLATE SYNTHASE / DUMP / TOMUDEX / ANTIFOLATE
Function / homology
Function and homology information


uracil metabolic process / Interconversion of nucleotide di- and triphosphates / intestinal epithelial cell maturation / pyrimidine nucleobase metabolic process / response to folic acid / tetrahydrofolate metabolic process / thymidylate synthase / sequence-specific mRNA binding / cartilage development / response to vitamin A ...uracil metabolic process / Interconversion of nucleotide di- and triphosphates / intestinal epithelial cell maturation / pyrimidine nucleobase metabolic process / response to folic acid / tetrahydrofolate metabolic process / thymidylate synthase / sequence-specific mRNA binding / cartilage development / response to vitamin A / heterocyclic compound binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / developmental growth / response to cytokine / liver regeneration / response to progesterone / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / circadian rhythm / response to toxic substance / regulation of translation / response to ethanol / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / mRNA binding / protein homodimerization activity / mitochondrion / nucleus / cytoplasm / 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
TOMUDEX / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSotelo-Mundo, R.R. / Ciesla, J. / Dzik, J.M. / Rode, W. / Maley, F. / Maley, G. / Hardy, L.W. / Montfort, W.R.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structures of rat thymidylate synthase inhibited by Tomudex, a potent anticancer drug.
Authors: Sotelo-Mundo, R.R. / Ciesla, J. / Dzik, J.M. / Rode, W. / Maley, F. / Maley, G.F. / Hardy, L.W. / Montfort, W.R.
History
DepositionJun 19, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 10, 2012Group: Non-polymer description
Revision 1.4Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: THYMIDYLATE SYNTHASE
C: THYMIDYLATE SYNTHASE
D: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,30712
Polymers140,2404
Non-polymers3,0678
Water1,35175
1
A: THYMIDYLATE SYNTHASE
B: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6536
Polymers70,1202
Non-polymers1,5334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-35 kcal/mol
Surface area22080 Å2
MethodPISA
2
C: THYMIDYLATE SYNTHASE
D: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6536
Polymers70,1202
Non-polymers1,5334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-33 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.700, 101.600, 140.800
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
THYMIDYLATE SYNTHASE


Mass: 35060.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P45352, thymidylate synthase
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-D16 / TOMUDEX / ZD1694 / Raltitrexed


Mass: 458.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22N4O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.59 Å3/Da / Density % sol: 52.1 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop contained 1:1 mixture of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
132 mg/mlprotein1drop
25 mMdithiothreitol1drop
320 mMTES1drop
46 mMdUMP1drop
56 mMTomudex1drop
620 %(w/v)mPEG50001reservoir
7200 mMammonium sulfate1reservoir
85 mMdithiothreitol1reservoir
9100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 1, 1998
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→8 Å / Num. obs: 35484 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 10.3
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.24 / % possible all: 71
Reflection shell
*PLUS
% possible obs: 71 % / Rmerge(I) obs: 0.214

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MADNESdata reduction
PROCORdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1689 5 %RANDOM
Rwork0.162 ---
obs0.162 33965 82.9 %-
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-8 Å
Luzzati sigma a0.36 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 208 75 9367
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.2
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_d1.02
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.151.5
X-RAY DIFFRACTIONx_mcangle_it4.842
X-RAY DIFFRACTIONx_scbond_it5.082
X-RAY DIFFRACTIONx_scangle_it7.262.5
LS refinement shellResolution: 2.6→2.64 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 72 5.2 %
Rwork0.241 1303 -
obs--66.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDODNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3TOMUDEX.PARTOMUDEX.TOP
X-RAY DIFFRACTION4PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.16 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.02
LS refinement shell
*PLUS
Rfactor obs: 0.241

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