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

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Basic information

Entry
Database: PDB / ID: 3eaw
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: 1.86 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 26, 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4266
Polymers35,9791
Non-polymers4465
Water2,810156
1
X: Thymidylate synthase
hetero molecules

X: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,85112
Polymers71,9582
Non-polymers89310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4110 Å2
ΔGint-18 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.704, 95.704, 81.940
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: 35979.211 Da / Num. of mol.: 1 / Mutation: V3Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pTS080 / 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.: 4 / 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.: 156 / 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: 20-25%ammonium sulfate, 20mM BME, 0.1M Tris PH8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 33751 / % possible obs: 91.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.061 / Χ2: 1.563 / Net I/σ(I): 35.545
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.392 / Num. unique all: 2093 / Χ2: 1 / % possible all: 57.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.277 / WRfactor Rwork: 0.234 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.769 / SU B: 3.777 / SU ML: 0.111 / SU R Cruickshank DPI: 0.141 / SU Rfree: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1691 5 %RANDOM
Rwork0.23 ---
obs0.232 33719 91.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 144.21 Å2 / Biso mean: 47.43 Å2 / Biso min: 20.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-0.7 Å20 Å2
2---1.4 Å20 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 24 156 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222175
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9782940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01723.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7515369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1191517
X-RAY DIFFRACTIONr_chiral_restr0.1530.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021647
X-RAY DIFFRACTIONr_nbd_refined0.2310.2953
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21438
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.212
X-RAY DIFFRACTIONr_mcbond_it1.4431.51330
X-RAY DIFFRACTIONr_mcangle_it2.36922075
X-RAY DIFFRACTIONr_scbond_it3.2283971
X-RAY DIFFRACTIONr_scangle_it4.8344.5865
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 65 -
Rwork0.317 1453 -
all-1518 -
obs--55.67 %

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