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

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Basic information

Entry
Database: PDB / ID: 3ebu
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: 2.05 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
DepositionAug 28, 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_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)36,3445
Polymers35,9931
Non-polymers3504
Water3,243180
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,68710
Polymers71,9872
Non-polymers7018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5570 Å2
ΔGint-86 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.616, 95.616, 81.616
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 / TSase / TS


Mass: 35993.262 Da / Num. of mol.: 1 / Mutation: V3T
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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris PH8.5, 35-40%ammonium sulfate, 20mM BME, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 26097 / % possible obs: 95.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Χ2: 3.573 / Net I/σ(I): 49.95
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.224 / Num. unique all: 2084 / Χ2: 2.575 / % possible all: 76.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementStarting model: PDB ENTRY 1HW3

1hw3


Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.793 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 2524 8.5 %
Rwork0.227 --
obs-25503 86.4 %
Solvent computationBsol: 76.014 Å2
Displacement parametersBiso max: 119.2 Å2 / Biso mean: 59.635 Å2 / Biso min: 30.47 Å2
Baniso -1Baniso -2Baniso -3
1--13.938 Å20 Å20 Å2
2---13.938 Å20 Å2
3---27.875 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 19 180 2313
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.184
X-RAY DIFFRACTIONc_mcbond_it1.8862
X-RAY DIFFRACTIONc_scbond_it3.0823
X-RAY DIFFRACTIONc_mcangle_it2.8062.5
X-RAY DIFFRACTIONc_scangle_it4.2783.5
LS refinement shellResolution: 2.05→2.12 Å
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramHicupCNS_TOPPAR:protein.topHIcup
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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