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- PDB-1tys: WATER-MEDIATED SUBSTRATE(SLASH)PRODUCT DISCRIMINATION: THE PRODUC... -

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Basic information

Entry
Database: PDB / ID: 1tys
TitleWATER-MEDIATED SUBSTRATE(SLASH)PRODUCT DISCRIMINATION: THE PRODUCT COMPLEX OF THYMIDYLATE SYNTHASE AT 1.83 ANGSTROMS
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 ...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, 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
DIHYDROFOLIC ACID / THYMIDINE-5'-PHOSPHATE / Thymidylate synthase / Thymidylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFauman, E. / Rutenber, E. / Stroud, R.
CitationJournal: Biochemistry / Year: 1994
Title: Water-mediated substrate/product discrimination: the product complex of thymidylate synthase at 1.83 A.
Authors: Fauman, E.B. / Rutenber, E.E. / Maley, G.F. / Maley, F. / Stroud, R.M.
History
DepositionMay 7, 1993Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)31,3093
Polymers30,5441
Non-polymers7662
Water2,954164
1
A: THYMIDYLATE SYNTHASE
hetero molecules

A: THYMIDYLATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6186
Polymers61,0872
Non-polymers1,5314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area7960 Å2
ΔGint-26 kcal/mol
Surface area18870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.970, 71.970, 115.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: RESIDUE CXM 1 IS A FORMATE GROUP BOUND TO N ATOM OF METHIONINE.
Components on special symmetry positions
IDModelComponents
11A-760-

HOH

21A-809-

HOH

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Components

#1: Protein THYMIDYLATE SYNTHASE


Mass: 30543.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P00470, UniProt: P0A884*PLUS, thymidylate synthase
#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-DHF / DIHYDROFOLIC ACID


Mass: 443.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE CXM 1 IS A FORMATE GROUP BOUND TO N ATOM OF METHIONINE
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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
1020 M1KPO4reservoir
120 mM1KPO4drop
53.8 mM1MgCl2drop
21.5 mg/mLTS C198(146)S1drop
31.9 mMH2folate1drop
81.25 M1(NH4)2SO4drop
45.8 mMdTMP1drop
92.5 M1(NH4)2SO4reservoir
63.8 mMdithiothreitol1drop
70.05 mMdisodium ethylenediaminetetraacetic acid1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 30830
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 9999 Å / Num. obs: 30830 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / Num. possible: 4845 / Num. unique obs: 3117 / Rmerge(I) obs: 0.312

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→7 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.183 -
obs0.183 30830
Refinement stepCycle: LAST / Resolution: 1.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 53 164 2370
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 30830 / Rfactor obs: 0.183 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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