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- PDB-3ef9: Replacement of Val3 in Human Thymidylate Synthase Affects Its Kin... -

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Basic information

Entry
Database: PDB / ID: 3ef9
TitleReplacement of Val3 in Human Thymidylate Synthase Affects Its Kinetic Properties and Intracellular Stability
ComponentsThymidylate synthase
KeywordsTRANSFERASE / Methyltransferase / Nucleotide biosynthesis
Function / homology
Function and homology information


thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription ...thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / mRNA regulatory element binding translation repressor activity / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / mitochondrion / nucleus / cytoplasm / cytosol
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 / Resolution: 3.2 Å
AuthorsHuang, X. / Gibson, L.M. / Bell, B.J. / Lovelace, L.L. / Pena, M.M. / Berger, F.G. / Berger, S.H.
CitationJournal: Biochemistry / Year: 2010
Title: Replacement of Val3 in human thymidylate synthase affects its kinetic properties and intracellular stability .
Authors: Huang, X. / Gibson, L.M. / Bell, B.J. / Lovelace, L.L. / Pena, M.M. / Berger, F.G. / Berger, S.H. / Lebioda, L.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)35,9693
Polymers35,7771
Non-polymers1922
Water48627
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9386
Polymers71,5542
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5180 Å2
ΔGint-72 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.349, 96.349, 83.561
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 / TS


Mass: 35776.965 Da / Num. of mol.: 1 / Mutation: V3L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.29, TS, TYMS / Plasmid: PTSO80 / Production host: Escherichia coli (E. coli) / Strain (production host): TX61- / 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.: 27 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris,PH8.5, 18%PEG4000,60mM ammonium sulfate, 20mM BME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 6685 / % possible obs: 75.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.195 / Χ2: 1.58 / Net I/σ(I): 5.364
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.1 % / Num. unique all: 194 / Χ2: 0.95 / % possible all: 22.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
CNSphasing
RefinementResolution: 3.2→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.752 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.298 620 8.1 %
Rwork0.252 --
obs-5705 74.2 %
Solvent computationBsol: 66.003 Å2
Displacement parametersBiso max: 171.67 Å2 / Biso mean: 69.314 Å2 / Biso min: 13.76 Å2
Baniso -1Baniso -2Baniso -3
1--5.896 Å20 Å20 Å2
2---5.896 Å20 Å2
3---11.792 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 10 27 2171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d2.277
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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