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- PDB-4jef: Crystal structure of human thymidylate synthase Y202A in inactive... -

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Basic information

Entry
Database: PDB / ID: 4jef
TitleCrystal structure of human thymidylate synthase Y202A in inactive conformation.
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Inactive form of human thymidylate synthase / hot spot residue
Function / homology
Function and homology information


uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / 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 / DNA biosynthetic process / G1/S-Specific Transcription / 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 / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / 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
Thymidylate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.311 Å
AuthorsTochowicz, A. / Stroud, R.M. / Wade, R.C.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase.
Authors: Salo-Ahen, O.M. / Tochowicz, A. / Pozzi, C. / Cardinale, D. / Ferrari, S. / Boum, Y. / Mangani, S. / Stroud, R.M. / Saxena, P. / Myllykallio, H. / Costi, M.P. / Ponterini, G. / Wade, R.C.
History
DepositionFeb 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2144
Polymers32,9261
Non-polymers2883
Water43224
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4288
Polymers65,8522
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area5170 Å2
ΔGint-86 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.955, 95.955, 82.649
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thymidylate synthase / / TS / TSase


Mass: 32925.785 Da / Num. of mol.: 1 / Mutation: Y202A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 2.0 M ammonium sulphate, 20 uM beta-ME, 0.1 M Mes, 5% (w/v) Peg 400, pH 6.5, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115879 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2008
RadiationMonochromator: KHOZU double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 2.31→37.002 Å / Num. obs: 19623 / % possible obs: 98.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.311→37.002 Å / SU ML: 0.69 / σ(F): 1.33 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1003 5.13 %
Rwork0.1848 --
obs0.1867 19569 99.57 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.836 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7071 Å20 Å20 Å2
2---0.7071 Å20 Å2
3---1.4142 Å2
Refinement stepCycle: LAST / Resolution: 2.311→37.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 15 24 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082080
X-RAY DIFFRACTIONf_angle_d1.1282812
X-RAY DIFFRACTIONf_dihedral_angle_d15.507783
X-RAY DIFFRACTIONf_chiral_restr0.07299
X-RAY DIFFRACTIONf_plane_restr0.005358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3107-2.43250.3791270.30152601X-RAY DIFFRACTION98
2.4325-2.58490.28421460.24922632X-RAY DIFFRACTION100
2.5849-2.78440.27731520.20982596X-RAY DIFFRACTION100
2.7844-3.06450.32961660.22472626X-RAY DIFFRACTION100
3.0645-3.50770.27691260.19672668X-RAY DIFFRACTION100
3.5077-4.41810.18881390.16762670X-RAY DIFFRACTION100
4.4181-37.00650.17911470.16372773X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 29.432 Å / Origin y: -35.6394 Å / Origin z: 2.2998 Å
111213212223313233
T0.3254 Å2-0.1046 Å20.0609 Å2-0.3934 Å2-0.0014 Å2--0.3416 Å2
L3.219 °20.8241 °2-0.3852 °2-4.47 °2-0.0724 °2--3.7635 °2
S-0.0761 Å °0.2712 Å °0.0479 Å °-0.4928 Å °0.193 Å °-0.3716 Å °0.1494 Å °0.1307 Å °-0.106 Å °
Refinement TLS groupSelection details: all

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