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- PDB-2fto: Y94F mutant of thymidylate synthase bound to thymidine-5'-phospha... -

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Basic information

Entry
Database: PDB / ID: 2fto
TitleY94F mutant of thymidylate synthase bound to thymidine-5'-phosphate and 10-propargyl-5,8-dideazafolid acid
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / 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
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / PHOSPHATE ION / THYMIDINE-5'-PHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Started with coordinates from isomorphous structure 1TSN / Resolution: 2 Å
AuthorsRoberts, S.A. / Montfort, W.R.
CitationJournal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006
Title: Structure of the Y94F mutant of Escherichia coli thymidylate synthase.
Authors: Roberts, S.A. / Hyatt, D.C. / Honts, J.E. / Changchien, L. / Maley, G.F. / Maley, F. / Montfort, W.R.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Oct 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

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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)31,5335
Polymers30,5441
Non-polymers9904
Water1,76598
1
X: Thymidylate synthase
hetero molecules

X: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,06710
Polymers61,0872
Non-polymers1,9798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8760 Å2
ΔGint-49 kcal/mol
Surface area19300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.080, 72.080, 115.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11X-327-

HOH

DetailsThe biological assembly is a dimer. There is a monomer in the asymmetric unit. The second monomer can be generated using the symmetry operation x-y,-y,2/3-z

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Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 30543.666 Da / Num. of mol.: 1 / Mutation: Y94F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thyA / Plasmid: BLUSCRIPT SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): Xac25 Thy / References: UniProt: P0A884, thymidylate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Chemical ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N5O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5 M ammonium sulfate, 20 mM KH2PO4, 4 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 17, 1996 / Details: graphite monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 24431 / Num. obs: 24431 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.069

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MADNESSdata reduction
PROCORdata scaling
RefinementMethod to determine structure: Started with coordinates from isomorphous structure 1TSN
Resolution: 2→8.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.94 / SU ML: 0.083 / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17917 979 5.1 %RANDOM
Rwork0.15807 ---
obs0.15919 18405 80.73 %-
all-19384 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.703 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2→8.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 66 98 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9723120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96924.211114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87115368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7381513
X-RAY DIFFRACTIONr_chiral_restr0.1010.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021773
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2848
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21521
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.981.51379
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6322159
X-RAY DIFFRACTIONr_scbond_it2.62831090
X-RAY DIFFRACTIONr_scangle_it4.1034.5958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 55 -
Rwork0.193 989 -
obs--59.66 %

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