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- PDB-4eb4: Crystal structure of mouse thymidylate synthase in ternary comple... -

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Basic information

Entry
Database: PDB / ID: 4eb4
TitleCrystal structure of mouse thymidylate synthase in ternary complex with dUMP and Tomudex
ComponentsThymidylate synthase
KeywordsTRANSFERASE / ternary complex / methyltransferase / Nucleotide biosynthesis
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...Interconversion of nucleotide di- and triphosphates / uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / heterocyclic compound binding / developmental growth / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / regulation of translation / methylation / response to ethanol / mitochondrial inner membrane / 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/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
TOMUDEX / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsDowiercial, A. / Jarmula, A. / Rypniewski, W.R. / Wilk, P. / Rode, W.
CitationJournal: Biomed Res Int / Year: 2014
Title: Crystal structure of mouse thymidylate synthase in tertiary complex with dUMP and raltitrexed reveals N-terminus architecture and two different active site conformations.
Authors: Dowiercial, A. / Wilk, P. / Rypniewski, W. / Rode, W. / Jarmula, A.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Non-polymer description
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Feb 28, 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)144,43725
Polymers140,0044
Non-polymers4,43321
Water22,0141222
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,62616
Polymers70,0022
Non-polymers2,62414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-43 kcal/mol
Surface area21810 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8129
Polymers70,0022
Non-polymers1,8107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-36 kcal/mol
Surface area22830 Å2
MethodPISA
3
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules

C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,43725
Polymers140,0044
Non-polymers4,43321
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area21490 Å2
ΔGint-95 kcal/mol
Surface area41970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.803, 114.216, 123.653
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Thymidylate synthase / TS / TSase


Mass: 35001.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tyms / Plasmid: pPIGDM4 / Production host: Escherichia coli (E. coli) / Strain (production host): TX61- / References: UniProt: P07607, thymidylate synthase

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Non-polymers , 7 types, 1243 molecules

#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 / Comment: chemotherapy, inhibitor*YM
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1222 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: MES, PEG 5K MME, (NH4)2SO4, DTT, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.73→20 Å / Num. obs: 148229 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Χ2: 0.987 / Net I/σ(I): 21
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.73-1.763.50.55672921.0041100
1.76-1.793.50.47873330.9511100
1.79-1.833.50.41673391.0281100
1.83-1.863.60.34373761.014199.9
1.86-1.93.60.28273371.0291100
1.9-1.953.60.22573471.011100
1.95-23.60.18473591.0221100
2-2.053.70.15673281.0161100
2.05-2.113.70.13374250.9671100
2.11-2.183.70.10773400.9411100
2.18-2.263.70.08974041.0631100
2.26-2.353.70.07473811.0251100
2.35-2.453.70.06673840.976199.9
2.45-2.583.70.05974310.9121100
2.58-2.743.70.05674090.8921100
2.74-2.963.70.05974310.9841100
2.96-3.253.70.06174900.994199.9
3.25-3.723.70.06474841.0611100
3.72-4.683.60.03775620.977199.9
4.68-203.50.0277770.874199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.79 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å20.04 Å
Translation2.5 Å20.04 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.268 / WRfactor Rwork: 0.2144 / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.8376 / SU B: 2.578 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1171 / SU Rfree: 0.1204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 7435 5 %RANDOM
Rwork0.19 140713 --
obs0.1924 148148 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 132.13 Å2 / Biso mean: 31.1915 Å2 / Biso min: 11.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9599 0 293 1222 11114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02210567
X-RAY DIFFRACTIONr_bond_other_d0.0010.027322
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.98814332
X-RAY DIFFRACTIONr_angle_other_deg1.016317807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66851269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35524.094513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05151807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9091569
X-RAY DIFFRACTIONr_chiral_restr0.1180.21474
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022172
X-RAY DIFFRACTIONr_mcbond_it1.231.56187
X-RAY DIFFRACTIONr_mcbond_other0.4031.52511
X-RAY DIFFRACTIONr_mcangle_it1.999210029
X-RAY DIFFRACTIONr_scbond_it2.86734380
X-RAY DIFFRACTIONr_scangle_it4.2254.54299
LS refinement shellResolution: 1.74→1.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 532 -
Rwork0.314 9725 -
all-10257 -
obs--95.59 %

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