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- PDB-4ein: Crystal structure of mouse thymidylate synthase in binary complex... -

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Basic information

Entry
Database: PDB / ID: 4ein
TitleCrystal structure of mouse thymidylate synthase in binary complex with a substrate analogue and strong inhibitor, N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate
ComponentsThymidylate synthase
KeywordsTransferase/Transferase Inhibitor / methyltransferase / Binding site / Catalysis / Dimerization / Transferase-Transferase Inhibitor complex
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 progesterone / response to cytokine / 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 / 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
Chem-NOH / Thymidylate synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3IHI structure was refined relative to collected diffraction data / Resolution: 1.75 Å
AuthorsDowiercial, A. / Jarmula, A. / Rypniewski, W.R. / Wilk, P. / Kierdaszuk, B. / Rode, W.
CitationJournal: PTERIDINES / Year: 2013
Title: Crystal structures of complexes of mouse thymidylate synthase crystallized with N4-OH-dCMP alone or in the presence of N5,10-methylenetetrahydrofolate
Authors: Dowiercial, A. / Jarmula, A. / Rypniewski, W.R. / Wilk, P. / Kierdaszuk, B. / Rode, W.
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / 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)70,7415
Polymers70,0022
Non-polymers7383
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-24 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.023, 87.956, 68.668
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-930-

HOH

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Components

#1: Protein Thymidylate synthase / / TS / TSase


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-NOH / 2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate)


Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 3.43 Å3/Da / Density % sol: 64.14 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: MES, PEG 8K, MgAcetate, 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: 1.75→20.06 Å / Num. obs: 90892 / % possible obs: 96.4 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.75-1.782.10.352197.6
1.78-1.812.10.318197.3
1.81-1.852.10.289197.7
1.85-1.892.10.275197.5
1.89-1.932.20.206197.4
1.93-1.972.20.194197.2
1.97-2.022.20.166197.8
2.02-2.072.20.148197.3
2.07-2.142.20.137197
2.14-2.22.20.12197.1
2.2-2.282.20.106196.9
2.28-2.372.20.101196.8
2.37-2.482.20.093196.2
2.48-2.612.20.087196.9
2.61-2.782.20.081196.1
2.78-2.992.30.076195.5
2.99-3.292.20.07195
3.29-3.762.30.059194.7
3.76-4.732.30.049194.5
4.73-202.30.036192.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: 3IHI structure was refined relative to collected diffraction data
Starting model: PDB entry 3IHI

3ihi


Resolution: 1.75→20.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.451 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1086 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25524 4570 5 %RANDOM
Rwork0.20594 ---
obs0.20846 86322 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.361 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 0 48 741 5389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224847
X-RAY DIFFRACTIONr_bond_other_d0.0010.023394
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.9696561
X-RAY DIFFRACTIONr_angle_other_deg1.00438224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4035582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13323.502237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53615842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8721537
X-RAY DIFFRACTIONr_chiral_restr0.120.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2971.52872
X-RAY DIFFRACTIONr_mcbond_other0.4011.51170
X-RAY DIFFRACTIONr_mcangle_it2.14524639
X-RAY DIFFRACTIONr_scbond_it2.94631975
X-RAY DIFFRACTIONr_scangle_it4.3794.51922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 290 -
Rwork0.306 5344 -
obs--80.29 %

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