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- PDB-3bfi: E. Coli Thymidylate Synthase Y209M mutant complexed with 5-nitro-dUMP -

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Basic information

Entry
Database: PDB / ID: 3bfi
TitleE. Coli Thymidylate Synthase Y209M mutant complexed with 5-nitro-dUMP
ComponentsThymidylate synthase
KeywordsTRANSFERASE / methyltransferase / Nucleotide biosynthesis / Repressor / RNA-binding / Translation regulation
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/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsRoberts, S.A. / Montfort, W.R.
CitationJournal: To be Published
Title: E.Coli thymidylate synthase complexed with 5-NITRO-2'-DEOXY URIDINE
Authors: Arendall, W.B. / Hyatt, D.C. / Roberts, S.A. / Dahlgran, A.L. / Maley, F. / Montfort, W.R.
History
DepositionNov 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)30,9793
Polymers30,5281
Non-polymers4512
Water1,49583
1
A: Thymidylate synthase
hetero molecules

A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9586
Polymers61,0552
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area4810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.020, 133.020, 133.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

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Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 30527.686 Da / Num. of mol.: 1 / Mutation: Y209M
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDU / 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE


Type: DNA linking / Mass: 355.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5 M AMMONIUM SULFATE, 20 MM REMARK 280 KH2PO4, 4 MM DTT, 4 MM 5-NO2-dUMP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Nov 13, 1997
RadiationMonochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. all: 19978 / Num. obs: 18431 / % possible obs: 93 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.46 Å / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MADNESSdata collection
PROCORdata reduction
PROCORdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3TMS

3tms


Resolution: 2.2→26.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.647 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21799 942 5.1 %RANDOM
Rwork0.1651 ---
obs0.16758 17489 92.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.051 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 28 83 2260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212248
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9533055
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11124.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34715356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3421513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021735
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2814
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21491
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9731.51362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71122140
X-RAY DIFFRACTIONr_scbond_it2.65631025
X-RAY DIFFRACTIONr_scangle_it4.2174.5915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 57 -
Rwork0.245 1130 -
obs--82.15 %

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