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- PDB-3bhl: E.coli thymidylate synthase complexes with 5-NO2dUMP and tetrahyd... -

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Basic information

Entry
Database: PDB / ID: 3bhl
TitleE.coli thymidylate synthase complexes with 5-NO2dUMP and tetrahydrofolate at 1.4 A resolution
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, 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
2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE / (6S)-5,6,7,8-TETRAHYDROFOLATE / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsRoberts, S.A. / Montfort, W.R.
CitationJournal: To be Published
Title: Structural Studies of Early Events in Catalysis by Thymidylate Synthase
Authors: Arendall III, W.B. / Hyatt, D.C. / Roberts, S.A. / Weichsel, A. / Dahlgren, A.L. / Maley, F. / Montfort, W.R.
History
DepositionNov 28, 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 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 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
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0099
Polymers61,1192
Non-polymers1,8897
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-40 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.870, 124.870, 66.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Thymidylate synthase / TS / TSase


Mass: 30559.666 Da / Num. of mol.: 2
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-NDU / 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE


Type: DNA linking / Mass: 355.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O10P
#3: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O6
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5 M ammonium sulfate, 20 mm KH2PO4, 4mm DTT, 4 mM 5-NO2dump, 4MM methylenetetrahydrofolate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 25, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→105.41 Å / Num. all: 115632 / Num. obs: 115632 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.6
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2TSC

2tsc


Resolution: 1.4→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.907 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20299 5799 5 %RANDOM
Rwork0.1742 ---
obs0.17564 109776 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.792 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 125 437 4868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214712
X-RAY DIFFRACTIONr_bond_other_d0.0020.023159
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9776421
X-RAY DIFFRACTIONr_angle_other_deg1.98437675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84524.667210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5211527
X-RAY DIFFRACTIONr_chiral_restr0.3020.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02983
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2332
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8541.52730
X-RAY DIFFRACTIONr_mcbond_other0.2491.51096
X-RAY DIFFRACTIONr_mcangle_it1.51124435
X-RAY DIFFRACTIONr_scbond_it2.27131982
X-RAY DIFFRACTIONr_scangle_it3.3944.51986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 434 -
Rwork0.225 8083 -
obs--99.85 %

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