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- PDB-4e5o: Crystal structure of mouse thymidylate synthase in complex with dUMP -

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Basic information

Entry
Database: PDB / ID: 4e5o
TitleCrystal structure of mouse thymidylate synthase in complex with dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / protein-ligand 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 / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to progesterone / response to cytokine / liver regeneration / response to toxic substance / circadian rhythm / regulation of translation / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / mRNA binding / protein homodimerization activity / mitochondrion / nucleus / cytosol / 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
1,4-BUTANEDIOL / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsDowiercial, A. / Jarmula, A. / Rypniewski, W. / Sokolowska, M. / Fraczyk, T. / Ciesla, J. / Rode, W.
Citation
Journal: Struct Chem / Year: 2016
Title: Mouse thymidylate synthase does not show the inactive conformation, observed for the human enzyme
Authors: Dowiercial, A. / Jarmula, A. / Wilk, P. / Rypniewski, W. / Kowalska, M. / Fraczyk, T. / Ciesla, J. / Rode, W.
#1: Journal: Pteridines / Year: 2009
Title: Crystal structures of substrate- and sulfate-bound mouse thymidylate synthase
Authors: Dowiercial, A. / Jarmula, A. / Rypniewski, W. / Sokolowska, M. / Fraczyk, T. / Ciesla, J. / Rode, W.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionApr 18, 2012ID: 3IHH
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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
E: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,43416
Polymers210,0066
Non-polymers2,42810
Water26,5181472
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6184
Polymers70,0022
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-35 kcal/mol
Surface area23340 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8897
Polymers70,0022
Non-polymers8875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-29 kcal/mol
Surface area22240 Å2
MethodPISA
3
E: Thymidylate synthase
F: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9275
Polymers70,0022
Non-polymers9253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-32 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.350, 88.540, 136.760
Angle α, β, γ (deg.)90.000, 95.990, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

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Components

#1: Protein
Thymidylate synthase / / TS / TSase


Mass: 35001.016 Da / Num. of mol.: 6
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
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1472 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: K/Na Tartrate, PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2008
RadiationMonochromator: Si(111) bent crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 207806 / % possible obs: 99.9 % / Rmerge(I) obs: 0.063 / Χ2: 0.955 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.730.993104100.9541100
1.73-1.760.836103230.9991100
1.76-1.790.744103760.9941100
1.79-1.830.701103511.0031100
1.83-1.870.612103131.0071100
1.87-1.910.41103821.0131100
1.91-1.960.263103480.8761100
1.96-2.020.18104070.851100
2.02-2.070.149103510.8571100
2.07-2.140.136103540.8341100
2.14-2.220.127103630.9881100
2.22-2.310.117103631.041100
2.31-2.410.1103960.934199.9
2.41-2.540.085104290.895199.9
2.54-2.70.074103321.118199.8
2.7-2.90.063104221.011199.8
2.9-3.20.05103810.868199.9
3.2-3.660.041104780.9011100
3.66-4.60.038104530.994199.8
4.6-200.047105740.982199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.95 Å
Translation2.5 Å19.95 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTS

1rts


Resolution: 1.7→19.95 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.3058 / WRfactor Rwork: 0.2486 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7769 / SU B: 2.855 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1348 / SU Rfree: 0.1395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.292 4109 2 %RANDOM
Rwork0.2347 ---
obs0.2358 205349 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 29.3331 Å2 / Biso min: 9.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13726 0 158 1472 15356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02214419
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.96919531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73751726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48223.612706
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77152475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.08415105
X-RAY DIFFRACTIONr_chiral_restr0.1450.22040
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111088
X-RAY DIFFRACTIONr_mcbond_it1.1741.58533
X-RAY DIFFRACTIONr_mcangle_it1.861213782
X-RAY DIFFRACTIONr_scbond_it2.93835886
X-RAY DIFFRACTIONr_scangle_it4.2214.55748
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.514 261 -
Rwork0.411 14492 -
all-14753 -
obs--97.21 %

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