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- PDB-4lhm: Thymidine phosphorylase from E.coli with 3'-azido-3'-deoxythymidine -

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Basic information

Entry
Database: PDB / ID: 4lhm
TitleThymidine phosphorylase from E.coli with 3'-azido-3'-deoxythymidine
ComponentsThymidine phosphorylase
KeywordsTRANSFERASE
Function / homology
Function and homology information


thymidine phosphorylase / pyrimidine nucleoside metabolic process / pyrimidine-nucleoside phosphorylase activity / thymidine metabolic process / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / AMP catabolic process / 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
3'-azido-3'-deoxythymidine / Thymidine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsTimofeev, V.I. / Abramchik, Y.A. / Esipov, R.S. / Kuranova, I.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: 3'-Azidothymidine in the active site of Escherichia coli thymidine phosphorylase: the peculiarity of the binding on the basis of X-ray study.
Authors: Timofeev, V. / Abramchik, Y. / Zhukhlistova, N. / Muravieva, T. / Fateev, I. / Esipov, R. / Kuranova, I.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal_grow / 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 / _exptl_crystal_grow.method / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Thymidine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,36511
Polymers47,2411
Non-polymers1,12410
Water8,755486
1
A: Thymidine phosphorylase
hetero molecules

A: Thymidine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,73022
Polymers94,4822
Non-polymers2,24820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area5220 Å2
ΔGint-182 kcal/mol
Surface area33400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.762, 130.762, 67.057
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 / TdRPase


Mass: 47240.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: deoA, tpp, ttg, b4382, JW4345 / Production host: Escherichia coli (E. coli) / References: UniProt: P07650, thymidine phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AZZ / 3'-azido-3'-deoxythymidine / Azidothymidine / Zidovudine


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Comment: medication, antiretroviral*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 298 K / Method: counter-diffusion / Details: COUNTER DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorDetector: CCD / Date: May 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.52→20 Å / Num. obs: 84887 / % possible obs: 99.85 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→14 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.734 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19578 4471 5 %RANDOM
Rwork0.15323 ---
obs0.15537 84887 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.982 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0 Å2-0 Å2
2---1.02 Å2-0 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.52→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 66 486 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193515
X-RAY DIFFRACTIONr_bond_other_d0.0010.023373
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9864775
X-RAY DIFFRACTIONr_angle_other_deg0.76737767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63324.296142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79115599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7481524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02749
X-RAY DIFFRACTIONr_rigid_bond_restr2.03436887
X-RAY DIFFRACTIONr_sphericity_free50.2665195
X-RAY DIFFRACTIONr_sphericity_bonded17.97557155

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