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- PDB-6y08: Mouse thymidylate synthase cocrystallized with dUMP and soaked in... -

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Basic information

Entry
Database: PDB / ID: 6y08
TitleMouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Fragment Screening / Fragment / Inhibitor / Thymidylate Synthase
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/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase
Similarity search - Domain/homology
Sulfamethoxazole / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å
AuthorsMaj, P. / Jarmula, A. / Wilk, P. / Weiss, M.S. / Rode, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/NZ1/00288 Poland
CitationJournal: To Be Published
Title: Mouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole
Authors: Maj, P. / Jarmula, A. / Wilk, P. / Weiss, M.S. / Rode, W.
History
DepositionFeb 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1256
Polymers70,0022
Non-polymers1,1234
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-31 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.545, 88.057, 68.262
Angle α, β, γ (deg.)90.000, 96.150, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Thymidylate synthase / / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P07607, thymidylate synthase
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-08D / Sulfamethoxazole / 4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide / SMX / SMZ / Sulfamethoxazole


Mass: 253.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11N3O3S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 64.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.15M Na/K Tartrate, 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.297→49.17 Å / Num. obs: 41996 / % possible obs: 99.4 % / Redundancy: 3.38 % / Biso Wilson estimate: 44.22 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.087 / Net I/σ(I): 12.73
Reflection shellResolution: 2.297→2.44 Å / Mean I/σ(I) obs: 1.95 / Num. unique obs: 6704 / CC1/2: 0.799 / Rrim(I) all: 0.662 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IHI

3ihi


Resolution: 2.297→49.169 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.8
RfactorNum. reflection% reflection
Rfree0.2496 2100 5 %
Rwork0.2103 --
obs0.2122 41987 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.67 Å2 / Biso mean: 48.055 Å2 / Biso min: 20.26 Å2
Refinement stepCycle: final / Resolution: 2.297→49.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4496 0 74 60 4630
Biso mean--48.16 39.82 -
Num. residues----557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2975-2.35090.36211360.3027259397
2.3509-2.40970.37431400.30472643100
2.4097-2.47490.36311400.29162662100
2.4749-2.54770.34231390.2982651100
2.5477-2.62990.39031390.29472648100
2.6299-2.72390.35591390.2746264199
2.7239-2.8330.3061400.2672264499
2.833-2.96190.26321400.2583266499
2.9619-3.1180.27171390.24422652100
3.118-3.31330.24921400.22962654100
3.3133-3.56910.29391410.21342671100
3.5691-3.92810.24641400.192663100
3.9281-4.49620.19431410.16142686100
4.4962-5.66340.15311420.1583268599
5.6634-49.1690.2131440.1736273099

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