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- PDB-4ead: Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideo... -

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Basic information

Entry
Database: PDB / ID: 4ead
TitleThymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine
ComponentsThymidine phosphorylase
KeywordsTransferase/Transferase inhibitor / Thymidine phosphorylase / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


thymidine phosphorylase / pyrimidine nucleoside metabolic process / thymidine metabolic process / 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
Chem-0NP / Thymidine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTimofeev, V.I. / Abramchik, Y.A. / Esipov, R.S. / Kuranova, I.P.
CitationJournal: To be Published
Title: Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine
Authors: Timofeev, V.I. / Abramchik, Y.A. / Esipov, R.S. / Kuranova, I.P.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Thymidine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,45812
Polymers47,2411
Non-polymers1,21711
Water9,368520
1
A: Thymidine phosphorylase
hetero molecules

A: Thymidine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,91624
Polymers94,4822
Non-polymers2,43422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area5950 Å2
ΔGint-166 kcal/mol
Surface area33080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.862, 129.862, 67.656
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: b4382, deoA, JW4345, tpp, ttg / Plasmid: pER-Thy1. / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07650, thymidine phosphorylase
#2: Chemical ChemComp-0NP / 2',3'-dideoxy-2'-fluoro-3'-triaza-1,2-dien-2-ium-1-yluridine


Mass: 272.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11FN5O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 273 K
Details: COUNTER DIFFUSION, LIQUID DIFFUSION, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 9, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 92521 / % possible obs: 99.8 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.5→1.51 Å / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.24 / Rsym value: 0.519 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TPT

2tpt


Resolution: 1.5→16 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.535 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.192 4617 5 %RANDOM
Rwork0.145 ---
obs0.147 87704 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å20 Å2
2---0.2 Å2-0 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.5→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 73 520 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193511
X-RAY DIFFRACTIONr_bond_other_d0.0040.0240
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9954745
X-RAY DIFFRACTIONr_angle_other_deg0.914380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14324.071140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56415598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9351525
X-RAY DIFFRACTIONr_chiral_restr0.0830.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212586
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr2.17733550
X-RAY DIFFRACTIONr_sphericity_free32.6145234
X-RAY DIFFRACTIONr_sphericity_bonded16.43153820
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 314 -
Rwork0.258 5948 -
obs--99.29 %

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