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- PDB-2tpt: STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUC... -

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Basic information

Entry
Database: PDB / ID: 2tpt
TitleSTRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE
ComponentsTHYMIDINE PHOSPHORYLASE
KeywordsTRANSFERASE / THYMIDINE PHOSPHORYLASE / SALVAGE PATHWAY
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 / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / 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 ...Thymidine phosphorylase / Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Pyrimidine nucleoside phosphorylase-like, C-terminal domain / 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 / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / 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 / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Thymidine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsPugmire, M.J. / Cook, W.J. / Jasanoff, A. / Walter, M.R. / Ealick, S.E.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase.
Authors: Pugmire, M.J. / Cook, W.J. / Jasanoff, A. / Walter, M.R. / Ealick, S.E.
#1: Journal: 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
DepositionNov 24, 1997Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3372
Polymers47,2411
Non-polymers961
Water0
1
A: THYMIDINE PHOSPHORYLASE
hetero molecules

A: THYMIDINE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6744
Polymers94,4822
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)132.000, 132.000, 67.200
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 /


Mass: 47240.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TETRAGONAL CRYSTAL FORM / Source: (natural) Escherichia coli (E. coli) / Strain: 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: 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

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1990
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→66 Å / Num. obs: 18521 / % possible obs: 94.8 % / Rsym value: 0.077
Reflection shellResolution: 2.58→2.67 Å / % possible all: 86.5
Reflection
*PLUS
% possible obs: 95.7 % / Num. measured all: 93897 / Rmerge(I) obs: 0.077

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Processing

Software
NameClassification
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.6→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.244 683 5 %RANDOM
Rwork0.207 ---
obs0.207 13181 95.7 %-
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 5 0 3311
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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