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- PDB-1tls: THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND METHYLENETETR... -

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Basic information

Entry
Database: PDB / ID: 1tls
TitleTHYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND METHYLENETETRAHYDROFOLATE
ComponentsTHYMIDYLATE SYNTHASE
KeywordsMETHYLTRANSFERASE / TRANSFERASE
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 ...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 / cytoplasm
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
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHyatt, D.C. / Maley, F. / Montfort, W.R.
CitationJournal: Biochemistry / Year: 1997
Title: Use of strain in a stereospecific catalytic mechanism: crystal structures of Escherichia coli thymidylate synthase bound to FdUMP and methylenetetrahydrofolate.
Authors: Hyatt, D.C. / Maley, F. / Montfort, W.R.
History
DepositionDec 3, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector / _software.name
Revision 1.4Mar 10, 2021Group: Advisory / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_site
Item: _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,6916
Polymers61,1192
Non-polymers1,5714
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-28 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.780, 126.780, 67.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.01, -0.012), (-0.016, -0.631, 0.775), (0.001, 0.775, 0.632)
Vector: 61.594, 22.794, -10.748)

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Components

#1: Protein THYMIDYLATE SYNTHASE /


Mass: 30559.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TERNARY COMPLEX WITH FDUMP (INHIBITOR) AND METHYLENETETRAHYDROFOLATE (COFACTOR)
Source: (gene. exp.) Escherichia coli (E. coli) / Description: STRAIN LACKS HOST THYMIDYLATE SYNTHASE GENE / Plasmid: BLUESCRIPT PLASMID SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): XAC 25
References: UniProt: P00470, UniProt: P0A884*PLUS, thymidylate synthase
#2: Chemical ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Fluorodeoxyuridylate


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12FN2O8P / Comment: inhibitor*YM
#3: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / Levomefolic acid


Mass: 459.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: CRYSTALLIZED BY VAPOR DIFFUSION FROM A SOLUTION OF 8MG/ML PROTEIN, 2MM FDUMP, 10MM CH2THF, 20MM PHOSPHATE PH 7.5, 4MM DTT, AND 1.05M AMMONIUM SULFATE; EQUILIBRATED AGAINST A SOLUTION OF 2. ...Details: CRYSTALLIZED BY VAPOR DIFFUSION FROM A SOLUTION OF 8MG/ML PROTEIN, 2MM FDUMP, 10MM CH2THF, 20MM PHOSPHATE PH 7.5, 4MM DTT, AND 1.05M AMMONIUM SULFATE; EQUILIBRATED AGAINST A SOLUTION OF 2.10M AMMONIUM SULFATE, 20MM PHOSPHATE PH 7.5, AND 4MM DTT., vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlE. coli TS1drop
22 mMFdUMP1drop
31 mM(6R,S)-CH2THF1drop
420 mMphosphate1drop
54 mMdithiothreitol1drop
61.05 Mammonium sulfate1drop
720 mMphosphate1reservoir
84 mMdithiothreitol1reservoir
92.1 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→14.8 Å / Num. obs: 18880 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.101 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.77 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1 / Rsym value: 0.434 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 63040 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.43

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Processing

Software
NameClassification
GPRLSArefinement
MADNESdata reduction
PROCORdata reduction
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TS.FDUMP.CB3717

Resolution: 2.6→14.8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.18 --
all-18880 -
obs-18880 99.5 %
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 108 194 4608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0440.033
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0650.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.681.75
X-RAY DIFFRACTIONp_mcangle_it2.7052.5
X-RAY DIFFRACTIONp_scbond_it1.9941.75
X-RAY DIFFRACTIONp_scangle_it3.2912.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.2090.2
X-RAY DIFFRACTIONp_singtor_nbd0.2070.3
X-RAY DIFFRACTIONp_multtor_nbd0.2160.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor35
X-RAY DIFFRACTIONp_staggered_tor19.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.715
X-RAY DIFFRACTIONp_special_tor010
Software
*PLUS
Name: 'GPRLSA' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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