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- PDB-3ihi: Crystal structure of mouse thymidylate synthase -

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Basic information

Entry
Database: PDB / ID: 3ihi
TitleCrystal structure of mouse thymidylate synthase
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 / thymidylate synthase / response to vitamin A / 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 / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / folic acid binding / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / heterocyclic compound binding / developmental growth / 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 / response to ethanol / methylation / mitochondrial inner membrane / 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, 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
Thymidylate synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsDowiercial, A. / Jarmula, A. / Rypniewski, W.R. / 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.R. / Sokolowska, M. / Fraczyk, T. / Ciesla, J. / Rode, W.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 6, 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1944
Polymers70,0022
Non-polymers1922
Water6,648369
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-19.1 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.202, 87.962, 68.043
Angle α, β, γ (deg.)90.000, 97.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thymidylate synthase / TSase / TS


Mass: 35001.016 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 278 K / Method: vapor diffusion
Details: Tris-HCl pH 8.5, PEG 4000, Li2SO4, VAPOR DIFFUSION, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2008
RadiationMonochromator: Bent germanium crystal, horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 1.94→20 Å / Num. obs: 69498 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.053 / Χ2: 1.027 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-1.973.40.61734760.937198.7
1.97-2.013.60.44534690.769199.8
2.01-2.053.60.31334830.79199.9
2.05-2.093.40.29534001.005196.9
2.09-2.143.50.26234311.011198.8
2.14-2.183.70.18635140.936199.9
2.18-2.243.70.16735170.989199.9
2.24-2.33.40.16633891.151196.9
2.3-2.373.70.12634730.94199.9
2.37-2.443.70.1135240.952199.9
2.44-2.533.70.09335110.984199.8
2.53-2.633.70.08534911.013199.9
2.63-2.753.60.07835041.16199.1
2.75-2.93.70.06634801.11199.9
2.9-3.083.70.05835061.191199.8
3.08-3.313.70.0535171.072199.8
3.31-3.643.60.04735151.174199.3
3.64-4.173.50.04434881.24198.8
4.17-5.243.60.03935011.12199.1
5.24-203.50.03733091.015191.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RTS

1rts


Resolution: 1.94→19.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.964 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1366 2 %RANDOM
Rwork0.22 ---
obs0.221 67377 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.25 Å2 / Biso mean: 41.367 Å2 / Biso min: 21.52 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4553 0 10 369 4932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224679
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.966328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34723.565230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47915809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1561534
X-RAY DIFFRACTIONr_chiral_restr0.1520.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213592
X-RAY DIFFRACTIONr_mcbond_it1.3781.52795
X-RAY DIFFRACTIONr_mcangle_it2.38824507
X-RAY DIFFRACTIONr_scbond_it3.49831884
X-RAY DIFFRACTIONr_scangle_it5.2414.51821
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 101 -
Rwork0.311 4846 -
all-4947 -
obs--99.4 %

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