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- PDB-4xr5: X-ray structure of the unliganded thymidine phosphorylase from Sa... -

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Basic information

Entry
Database: PDB / ID: 4xr5
TitleX-ray structure of the unliganded thymidine phosphorylase from Salmonella typhimurium at 2.05 A resolution
ComponentsThymidine phosphorylase
KeywordsTRANSFERASE / thymidine phosphorylase / nucleoside / metabolism
Function / homology
Function and homology information


thymidine phosphorylase / pyrimidine-nucleoside phosphorylase activity / thymidine metabolic process / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / AMP catabolic process / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Thymidine phosphorylase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsBalaev, V.V. / Lashkov, A.A. / Gabdulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research14-04-00952 Russian Federation
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine.
Authors: Balaev, V.V. / Lashkov, A.A. / Gabdulkhakov, A.G. / Dontsova, M.V. / Seregina, T.A. / Mironov, A.S. / Betzel, C. / Mikhailov, A.M.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thymidine phosphorylase
B: Thymidine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6917
Polymers94,0992
Non-polymers5925
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-6 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.942, 171.213, 45.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Thymidine phosphorylase / TdRPase


Mass: 47049.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: deoA, STM4568 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CP66, thymidine phosphorylase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium thiocyanate, 0.1 M Bis Tris propane, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.05→47.72 Å / Num. all: 58911 / Num. obs: 58911 / % possible obs: 95.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 15.7
Reflection shellResolution: 2.05→2.08 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.021 / Mean I/σ(I) obs: 3.3 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X46

4x46


Resolution: 2.05→47.716 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 2735 5 %Random selection
Rwork0.2212 51931 --
obs0.2225 54666 95.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.21 Å2 / Biso mean: 51.8461 Å2 / Biso min: 23.03 Å2
Refinement stepCycle: final / Resolution: 2.05→47.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 38 89 6709
Biso mean--61.31 47.13 -
Num. residues----880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096717
X-RAY DIFFRACTIONf_angle_d1.2759072
X-RAY DIFFRACTIONf_chiral_restr0.0511051
X-RAY DIFFRACTIONf_plane_restr0.0061185
X-RAY DIFFRACTIONf_dihedral_angle_d16.282476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.08540.38631380.33632609274797
2.0854-2.12330.35411360.33772573270997
2.1233-2.16410.35771340.3272560269495
2.1641-2.20830.36371380.32582604274298
2.2083-2.25630.33711340.3142550268494
2.2563-2.30880.37511340.31932560269497
2.3088-2.36650.32531360.30112584272096
2.3665-2.43050.35151370.29492583272097
2.4305-2.5020.31511360.29622583271995
2.502-2.58280.32041370.2812612274997
2.5828-2.67510.32571370.28432594273195
2.6751-2.78220.31241390.27842638277798
2.7822-2.90880.29091350.26562580271596
2.9088-3.06210.25471370.25622605274295
3.0621-3.25390.24491370.23732600273795
3.2539-3.50510.24431370.21152589272695
3.5051-3.85770.20691370.18422617275495
3.8577-4.41560.18081360.16122583271993
4.4156-5.56180.21481360.16022587272392
5.5618-47.72850.17361440.16442720286492
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5055-0.9764-0.35950.99570.16950.30180.0490.35120.3401-0.1675-0.0638-0.1934-0.0898-0.0193-0.01030.3383-0.01730.00870.38870.19990.546414.390638.8613-23.8302
21.3163-0.7586-0.06550.94280.63020.198-0.07510.39710.121-0.110.0502-0.1641-0.03180.04280.00460.3697-0.03290.00220.40140.19910.53812.492344.139-20.331
32.57380.38090.49361.2430.2021.0103-0.02790.04720.18720.1440.01820.05860.0019-0.05860.02180.3411-0.00060.0210.2910.19240.4972-13.881146.883-12.7494
42.4601-0.36670.07991.33440.54760.54820.02320.5634-0.1830.0129-0.08480.43320.1505-0.07290.05650.3556-0.00810.04370.3968-0.010.342813.21272.7152-32.4342
51.4635-0.7246-0.39260.4831-0.38661.16250.24660.31330.1177-0.1279-0.30980.4627-0.1129-0.1350.04710.5072-0.0108-0.04421.0152-0.17390.449322.8334-5.7204-50.3018
61.5786-1.2584-0.48441.4338-0.51970.56490.05990.49050.2788-0.05090.02770.1182-0.071-0.01490.03290.36370.01440.02860.4122-0.00210.274322.38673.3694-31.4014
73.28960.6158-0.10671.04040.25020.59680.01951.0796-0.0332-0.23830.01110.0847-0.0194-0.0942-0.00310.39880.0488-0.01570.6334-0.0570.161240.7062-1.8392-43.3605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 105 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 252 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 440 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 105 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 106 through 161 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 162 through 230 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 231 through 440 )B0

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