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- PDB-5ey3: X-ray structure of the thymidine phosphorylase from Salmonella ty... -

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Basic information

Entry
Database: PDB / ID: 5ey3
TitleX-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate
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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / Thymidine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.905 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: To Be Published
Title: X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate
Authors: Balaev, V.V. / Lashkov, A.A. / Gabdulkhakov, A.G. / Betzel, C. / Mikhailov, A.M.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)95,74215
Polymers94,3882
Non-polymers1,35413
Water4,522251
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-104 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.398, 193.398, 58.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thymidine phosphorylase / TdRPase


Mass: 47193.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The A chain contains two residues of the thrombine restriction site (Gly and Ser). In the B chain we could not localize those residues due to poor electron density map of the N-terminal residues.
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: deoA, STM4568 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CP66, thymidine phosphorylase

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Non-polymers , 5 types, 264 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M BICINE, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionNumber: 535931 / Rmerge(I) obs: 0.095 / Χ2: 1.02 / D res high: 1.9 Å / D res low: 48.29 Å / Num. obs: 79998 / % possible obs: 94.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
5.6848.29333110.021
4.035.68581110.027
3.294.03746710.045
2.853.29875710.079
2.552.85996710.149
2.332.551092810.247
2.162.33766710.497
2.022.161274210.674
1.92.021332811.122
ReflectionResolution: 1.905→136.753 Å / Num. all: 80208 / Num. obs: 80208 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 25.28 Å2 / Rmerge F obs: 0.999 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Rsym value: 0.095 / Χ2: 1.02 / Net I/av σ(I): 7.9 / Net I/σ(I): 16.4 / Num. measured all: 537407
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible allRmerge F obsNum. measured obsNum. possibleNum. unique obsRrim(I) all
1.905-2.016.81.2070.682530122220.51.2071.899.5
2.01-2.136.70.7321.177257115880.3060.7322.81000.7899003313590133281.216
2.13-2.286.60.5791.34823273510.2440.5793.667.40.8758416112743127420.731
2.28-2.466.90.3032.66538795360.1240.3036.693.40.921512551189576670.538
2.46-2.696.50.1864.26120893530.0790.1869.81000.9767422610930109280.267
2.69-3.0170.1146.85963684890.0460.11415.81000.99167261996899670.162
3.01-3.486.60.06112.54982775150.0260.06126.81000.99760179875887570.085
3.48-4.266.70.03918.64269363820.0160.03943.81000.99948692747774670.049
4.26-6.026.60.02624.93268549750.0110.02655.71000.99938412581258110.029
6.02-48.296.40.0229.41795227970.0090.0266.999.6121712334933310.023

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XR5

4xr5


Resolution: 1.905→48.29 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 3856 4.81 %Random selection
Rwork0.2 76247 --
obs0.2018 80103 94.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.36 Å2 / Biso mean: 35.7813 Å2 / Biso min: 15.15 Å2
Refinement stepCycle: final / Resolution: 1.905→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6581 0 78 254 6913
Biso mean--50.12 34.74 -
Num. residues----882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066743
X-RAY DIFFRACTIONf_angle_d0.7859121
X-RAY DIFFRACTIONf_chiral_restr0.0491055
X-RAY DIFFRACTIONf_plane_restr0.0051182
X-RAY DIFFRACTIONf_dihedral_angle_d16.7684057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9048-1.9280.58771460.56552793293998
1.928-1.95240.46741340.43792789292398
1.9524-1.97810.32691370.303428653002100
1.9781-2.00520.32181480.272628432991100
2.0052-2.03390.32541550.261328332988100
2.0339-2.06420.29631290.24528682997100
2.0642-2.09650.28771410.244928282969100
2.0965-2.13090.27461460.23928883034100
2.1309-2.16760.30121610.234528252986100
2.1676-2.2070.28671380.228628362974100
2.207-2.24950.2725510.24071219127093
2.2495-2.29540.3036310.23251754891
2.2954-2.34530.2661630.210928373000100
2.3453-2.39980.23871400.212828572997100
2.3998-2.45980.22861430.204228853028100
2.4598-2.52640.23681510.196528533004100
2.5264-2.60070.24311570.203128172974100
2.6007-2.68460.22261560.199628803036100
2.6846-2.78060.24031400.199328623002100
2.7806-2.89190.22011510.199628873038100
2.8919-3.02350.23961280.204628672995100
3.0235-3.18290.20951340.206529023036100
3.1829-3.38220.22821380.189429043042100
3.3822-3.64330.21751260.175828873013100
3.6433-4.00980.18551710.167928513022100
4.0098-4.58960.18791550.142729123067100
4.5896-5.78090.21461350.159229483083100
5.7809-48.30580.20481510.165529943145100

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