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- PDB-5x4y: Mutant human thymidylate synthase M190K crystallized in a sulfate... -

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Basic information

Entry
Database: PDB / ID: 5x4y
TitleMutant human thymidylate synthase M190K crystallized in a sulfate-containing condition
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


uracil metabolic process / intestinal epithelial cell maturation / Interconversion of nucleotide di- and triphosphates / response to folic acid / thymidylate synthase / sequence-specific mRNA binding / response to vitamin A / tetrahydrofolate interconversion / thymidylate synthase activity / cartilage development ...uracil metabolic process / intestinal epithelial cell maturation / Interconversion of nucleotide di- and triphosphates / response to folic acid / thymidylate synthase / sequence-specific mRNA binding / response to vitamin A / tetrahydrofolate interconversion / thymidylate synthase activity / cartilage development / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / response to glucocorticoid / response to cytokine / mRNA regulatory element binding translation repressor activity / response to progesterone / 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, 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, D. / Jansson, A. / Larsson, A. / Nordlund, P.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Nanyang Technological UniversityM060080004.70301200 Singapore
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of human thymidylate synthase reveal a site that may control conformational switching between active and inactive states
Authors: Chen, D. / Jansson, A. / Sim, D. / Larsson, A. / Nordlund, P.
History
DepositionFeb 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0403
Polymers35,8481
Non-polymers1922
Water2,522140
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0806
Polymers71,6962
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area4860 Å2
ΔGint-71 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.951, 95.951, 80.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thymidylate synthase / TSase


Mass: 35847.996 Da / Num. of mol.: 1 / Mutation: M190K
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


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.: 140 / 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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100mM MES, pH 6.5, 1.6M ammonium sulfate, 10% 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→83.096 Å / Num. all: 22239 / Num. obs: 22239 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Rsym value: 0.062 / Net I/av σ(I): 9.4 / Net I/σ(I): 26.7 / Num. measured all: 263957
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.32120.35523825232000.1070.3710.3557.7100
2.32-2.4612.10.2353.23692430510.070.2450.23510100
2.46-2.6312.10.1724.43422528360.0510.1790.17213.2100
2.63-2.8412.10.1116.73224526720.0330.1160.11119.6100
2.84-3.11120.0789.32954724630.0240.0820.07826.5100
3.11-3.48120.05512.32678022390.0170.0570.05537.2100
3.48-4.0211.80.04414.32362119980.0130.0460.04447.9100
4.02-4.9211.70.03716.21953916760.0110.0390.03758100
4.92-6.9611.30.04113.61517813420.0130.0430.04149.6100
6.96-26.963100.0262376467620.0080.0270.0265498.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HW3

1hw3


Resolution: 2.2→83.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.577 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 1136 5.1 %RANDOM
Rwork0.1868 ---
obs0.1893 21018 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.8 Å2 / Biso mean: 38.615 Å2 / Biso min: 15 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.38 Å20 Å2
2---0.75 Å20 Å2
3---2.44 Å2
Refinement stepCycle: final / Resolution: 2.2→83.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 10 140 2365
Biso mean--58.11 40.95 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192279
X-RAY DIFFRACTIONr_bond_other_d0.0020.022118
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9613087
X-RAY DIFFRACTIONr_angle_other_deg1.0534866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6935276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62223.514111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69315376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8441517
X-RAY DIFFRACTIONr_chiral_restr0.1190.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212574
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02545
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 71 -
Rwork0.375 1514 -
all-1585 -
obs--98.39 %

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