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

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Basic information

Entry
Database: PDB / ID: 1tsn
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 / 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
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / PHOSPHATE ION / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Thymidylate synthase / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 2, 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: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Apr 3, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4404
Polymers30,5601
Non-polymers8813
Water1,982110
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8818
Polymers61,1192
Non-polymers1,7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8240 Å2
ΔGint-36 kcal/mol
Surface area19070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.100, 72.100, 115.270
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
11A-332-

HOH

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30559.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TERNARY COMPLEX WITH FDUMP (INHIBITOR) AND METHYLENETETRAHYDROFOLATE (COFACTOR)
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P00470, UniProt: P0A884*PLUS, thymidylate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-UFP / 5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 326.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12FN2O8P
#4: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growMethod: vapor diffusion / pH: 8
Details: CRYSTALLIZED BY VAPOR DIFFUSION FROM A SOLUTION OF 8MG/ML PROTEIN, 2MM FDUMP, 10MM CH2THF, 20MM PHOSPHATE PH 8.0, 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 8.0, 4MM DTT, AND 1.05M AMMONIUM SULFATE; EQUILIBRATED AGAINST A SOLUTION OF 2.10M AMMONIUM SULFATE, 20MM PHOSPHATE PH 8.0, 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: 2.2→9 Å / Num. obs: 18104 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.095 / Net I/σ(I): 6.4
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.355 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 76346 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
Rmerge(I) obs: 0.36

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Processing

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

Resolution: 2.2→9 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.178 --
all-18104 -
obs-18104 98 %
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 59 110 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.050.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6031.75
X-RAY DIFFRACTIONp_mcangle_it2.4172.5
X-RAY DIFFRACTIONp_scbond_it2.2781.75
X-RAY DIFFRACTIONp_scangle_it3.6542.5
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.2230.2
X-RAY DIFFRACTIONp_singtor_nbd0.210.3
X-RAY DIFFRACTIONp_multtor_nbd0.2140.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.55
X-RAY DIFFRACTIONp_staggered_tor17.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.315
X-RAY DIFFRACTIONp_special_tor010
Software
*PLUS
Name: GPRLSA / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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