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- PDB-4txj: Crystal structure of uridine phosphorylase from Schistosoma manso... -

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Basic information

Entry
Database: PDB / ID: 4txj
TitleCrystal structure of uridine phosphorylase from Schistosoma mansoni in complex with thymidine
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Uridine phosphorylase thymidine
Function / homology
Function and homology information


uridine catabolic process / nucleotide catabolic process / uridine phosphorylase / uridine phosphorylase activity / UMP salvage / identical protein binding / cytosol
Similarity search - Function
Uridine phosphorylase, eukaryotic / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE / Uridine phosphorylase A
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.662 Å
AuthorsTorini, J. / Marinho, A. / Romanello, L. / Cassago, A. / DeMarco, R. / Brandao-Neto, J. / Pereira, H.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
CitationJournal: Biochimie / Year: 2016
Title: Analysis of two Schistosoma mansoni uridine phosphorylases isoforms suggests the emergence of a protein with a non-canonical function.
Authors: da Silva Neto, A.M. / Torini de Souza, J.R. / Romanello, L. / Cassago, A. / Serrao, V.H. / DeMarco, R. / Brandao-Neto, J. / Garratt, R.C. / Pereira, H.D.
History
DepositionJul 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Apr 17, 2019Group: Author supporting evidence / Data collection / Polymer sequence
Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_target_identifier / _pdbx_audit_support.funding_organization
Revision 2.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Sep 27, 2023Group: 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
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: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,95212
Polymers130,5984
Non-polymers1,3538
Water19,3661075
1
A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9766
Polymers65,2992
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-75 kcal/mol
Surface area21530 Å2
MethodPISA
2
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9766
Polymers65,2992
Non-polymers6774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-77 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.820, 108.080, 116.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Uridine phosphorylase


Mass: 32649.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_082430 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4VGI0, uridine phosphorylase
#2: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2O5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1075 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200mM Ammonium suphate, 100mM Bis-Tris pH5.5, 20-25% Peg3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 1.66→79.09 Å / Num. obs: 141838 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 14.08 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-IDRejects% possible all
1.66-1.74.50.5932.110100
7.43-79.094.10.0741098.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
GDAdata collection
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EUE

3eue


Resolution: 1.662→79.09 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 7110 5.02 %Random selection
Rwork0.1859 134639 --
obs0.1871 141749 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.92 Å2 / Biso mean: 14.026 Å2 / Biso min: 3.37 Å2
Refinement stepCycle: final / Resolution: 1.662→79.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8966 0 88 1075 10129
Biso mean--13.45 27.23 -
Num. residues----1158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019288
X-RAY DIFFRACTIONf_angle_d1.06812563
X-RAY DIFFRACTIONf_chiral_restr0.271452
X-RAY DIFFRACTIONf_plane_restr0.0041600
X-RAY DIFFRACTIONf_dihedral_angle_d12.1713357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.662-1.68060.30532410.240444874728100
1.6806-1.70040.23822300.22344234653100
1.7004-1.72110.24062390.221144484687100
1.7211-1.74290.26592020.220845064708100
1.7429-1.76580.23282270.214544524679100
1.7658-1.790.23942540.206744114665100
1.79-1.81560.24282270.195544654692100
1.8156-1.84270.24532670.197544314698100
1.8427-1.87150.22282610.193944414702100
1.8715-1.90220.2382470.187644214668100
1.9022-1.9350.2142250.184544814706100
1.935-1.97020.21062450.179844354680100
1.9702-2.00810.20032410.177544814722100
2.0081-2.0490.23382210.184344474668100
2.049-2.09360.20672250.176244994724100
2.0936-2.14230.21992170.174144574674100
2.1423-2.19590.18282310.167544924723100
2.1959-2.25530.19542400.167644834723100
2.2553-2.32160.19792190.176144874706100
2.3216-2.39660.20192660.181244814747100
2.3966-2.48220.1852250.174344874712100
2.4822-2.58160.22242220.179145154737100
2.5816-2.69910.20232360.186244924728100
2.6991-2.84140.2142330.187145144747100
2.8414-3.01950.20752500.184744724722100
3.0195-3.25260.20252380.185145264764100
3.2526-3.57990.21142320.17884520475299
3.5799-4.09790.19752290.17554566479599
4.0979-5.16280.18662760.17664564484099
5.1628-79.18460.22562440.21074755499999
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)
12.56320.7576-0.27881.0025-0.411.3182-0.0110.22920.0568-0.11920.02470.2046-0.0436-0.244-0.03140.10140.0241-0.02060.0993-0.03010.1107-36.958623.066-18.0013
20.68930.09240.0431.1448-0.07820.6448-0.02890.1079-0.0374-0.07890.0325-0.00690.00370.00940.00080.06870.009-0.00630.0783-0.02110.0617-21.51219.1626-15.2533
30.5301-0.1179-0.06770.6551-0.23180.9904-0.0097-0.016-0.06-0.0287-0.0127-0.09620.07420.11660.02140.0640.0162-0.00010.0897-0.01870.1058-11.232914.7373-9.5666
41.989-0.1106-0.21110.86760.21521.4592-0.0479-0.1490.12670.0650.0338-0.0757-0.03650.0986-0.01310.0956-0.0024-0.02750.0576-0.01430.0905-21.372920.834414.3061
50.84350.15410.04080.58270.06210.7314-0.0129-0.0515-0.04420.0578-0.02770.03960.0559-0.07990.03960.0717-0.00190.01220.0621-0.00740.09-36.32849.52856.5854
64.0886-2.7441-0.56896.35881.81692.1632-0.04310.2663-0.34940.10710.0870.23350.48790.011-0.01610.2887-0.0426-0.07960.1730.00060.15914.6205-35.0736-0.7837
70.5310.4435-0.42881.6804-0.18881.00020.11950.0991-0.0901-0.14260.03890.38690.2469-0.3834-0.11370.1527-0.0314-0.07550.18630.0050.20495.755-20.01-11.6585
81.76060.40061.65431.79250.99542.82930.0165-0.1194-0.0134-0.0586-0.00110.27540.0096-0.31540.0290.1053-0.0242-0.04940.11890.00640.12228.5219-18.9268-5.8651
90.82880.37060.06831.4003-0.28090.77740.02850.0446-0.0933-0.16680.05760.00420.1250.0598-0.08650.11140.0181-0.01380.1166-0.03070.089220.8328-16.8663-9.1786
100.47030.2481-0.47921.7732-0.95531.23210.0606-0.0161-0.0820.0058-0.1301-0.27350.21270.32230.04380.13440.0705-0.03090.2367-0.04290.155933.7631-20.8992-2.3951
111.97620.60550.71942.37561.00584.6034-0.06130.36740.0541-0.46620.13160.0369-0.3310.0009-0.08730.162-0.01640.01740.1978-0.01180.097423.6985-6.6199-20.9345
120.76980.2120.33410.74630.45191.06240.04170.0764-0.0186-0.02420.0303-0.1090.0150.1802-0.07260.0887-0.00540.00180.1179-0.01620.08528.536-4.9928-2.7565
130.64460.46990.13821.93130.71891.9131-0.00480.17710.0536-0.3778-0.08120.2056-0.0504-0.16270.09820.12970.0256-0.04120.1698-0.01080.124411.4798-7.7891-17.9107
140.62190.5011-0.511.4334-0.61791.34390.0583-0.04820.12750.23780.12290.2606-0.1647-0.1448-0.13770.12680.04090.03120.12250.01410.135610.6104-0.41515.2042
150.84570.0231-0.08431.2189-0.4081.09540.0503-0.0476-0.01830.16350.02780.0075-0.04090.0371-0.06930.1149-0.0009-0.01240.0861-0.00890.072920.0779-11.611616.1838
160.8343-0.24270.01881.09840.17121.25980.0112-0.0828-0.12960.09640.05690.11950.1517-0.036-0.06310.14440.0021-0.02350.11090.03160.118416.5107-23.969119.2023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 47 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 179 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 296 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 83 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 296 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 7 through 24 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 25 through 71 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 72 through 94 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 95 through 142 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 143 through 166 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 167 through 193 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 194 through 268 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 269 through 296 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 71 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 72 through 166 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 167 through 296 )D0

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