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- PDB-1tpt: THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHE... -

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Basic information

Entry
Database: PDB / ID: 1tpt
TitleTHREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION
ComponentsTHYMIDINE PHOSPHORYLASE
KeywordsTHYMIDINE PHOSPHORYLASE
Function / homology
Function and homology information


thymidine phosphorylase / pyrimidine nucleoside metabolic process / thymidine metabolic process / pyrimidine-nucleoside phosphorylase activity / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / DNA damage response / membrane / cytosol
Similarity search - Function
Thymidine phosphorylase / Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Glycosyl transferase family 3, N-terminal domain ...Thymidine phosphorylase / Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily
Similarity search - Domain/homology
THYMINE / Thymidine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsWalter, M.R. / Cook, W.J. / Cole, L.B. / Short, S.A. / Koszalka, G.W. / Krenitsky, T.A. / Ealick, S.E.
CitationJournal: J.Biol.Chem. / Year: 1990
Title: Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 A resolution.
Authors: Walter, M.R. / Cook, W.J. / Cole, L.B. / Short, S.A. / Koszalka, G.W. / Krenitsky, T.A. / Ealick, S.E.
History
DepositionJun 14, 1990Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4633
Polymers47,2411
Non-polymers2222
Water0
1
A: THYMIDINE PHOSPHORYLASE
hetero molecules

A: THYMIDINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9266
Polymers94,4822
Non-polymers4444
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)133.000, 133.000, 67.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein THYMIDINE PHOSPHORYLASE / / Coordinate model: Cα atoms only


Mass: 47240.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P07650, thymidine phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TDR / THYMINE / Thymine


Mass: 126.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Details: took from Cook, W.J.,(1987) J. Biol. Chem., 262, 3788.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
152 mg/mlprotein1drop
235 %ammonium sulfate1drop
30.05 Mcitrate1drop
435 %ammonium sulfate1reservoir
50.05 Mcitrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 15034 / Num. measured all: 77819 / Rmerge F obs: 0.082

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.28 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 14 0 454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_deg1.5
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg

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