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

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Basic information

Entry
Database: PDB / ID: 4txm
TitleCrystal structure of uridine phosphorylase from Schistosoma mansoni in complex with thymine
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / Uridine phosphorylase
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
THYMINE / Uridine phosphorylase A
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsMarinho, A. / Torini, J. / 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 1.0Oct 14, 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
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
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 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7446
Polymers65,2992
Non-polymers4444
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-79 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.361, 84.872, 87.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Uridine phosphorylase


Mass: 32649.598 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200mM ammonium sulphate, 100mM Bis-Tris pH5.5, 20-25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9136 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9136 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 43916 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge F obs: 0.143 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.119 / Χ2: 1.022 / Net I/av σ(I): 10.1 / Net I/σ(I): 10.1 / Num. measured all: 209662
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.93-2.040.6560.592.4428218720463960.66888.8
2.04-2.190.3910.4343.8236186677967140.48299
2.19-2.360.2610.3155.3433301633962730.35199
2.36-2.580.1730.2187.3429491584757920.24499.1
2.58-2.890.130.1499.5823924528452170.16898.7
2.89-3.330.0750.09714.1921422472646340.10998.1
3.33-4.080.0390.05720.8817049402139890.06599.2
4.08-5.750.030.04324.611917315730580.04996.9
5.750.0210.03828.298154186918430.04298.6

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
GDAdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TXJ

4txj


Resolution: 1.93→42.436 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 26.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 2195 5 %Random selection
Rwork0.2144 41701 --
obs0.2163 43896 97.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.14 Å2 / Biso mean: 34.3136 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 1.93→42.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 28 455 4735
Biso mean--21.43 37.94 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034353
X-RAY DIFFRACTIONf_angle_d0.675888
X-RAY DIFFRACTIONf_chiral_restr0.025682
X-RAY DIFFRACTIONf_plane_restr0.003756
X-RAY DIFFRACTIONf_dihedral_angle_d11.0321511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.96970.36561070.29462038214577
1.9697-2.01550.30811330.27092529266297
2.0155-2.06590.30581370.24952590272798
2.0659-2.12180.26561370.24472619275699
2.1218-2.18420.28651380.2372621275999
2.1842-2.25470.29521390.22692625276499
2.2547-2.33530.27041380.22022625276399
2.3353-2.42880.28971400.21152649278999
2.4288-2.53930.26941370.22322629276699
2.5393-2.67320.25971400.22262657279799
2.6732-2.84060.24581410.22752680282199
2.8406-3.05990.22271350.21882556269196
3.0599-3.36770.28971410.21512684282599
3.3677-3.85480.23011420.18972697283999
3.8548-4.85550.20431430.18612726286999
4.8555-42.44630.2261470.20312776292397
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)
10.4469-0.7284-0.52311.6744-0.28292.50670.16640.03920.01050.3975-0.0371-0.41590.89930.453-0.04010.41160.1059-0.09610.25250.0010.28031.2425-16.93119.4702
20.7022-0.10770.49561.9184-0.57252.07140.05170.1472-0.05030.24680.0811-0.50140.46460.5055-0.08490.26450.0913-0.09390.2613-0.03420.27880.9962-12.83028.0866
30.55850.5417-0.38433.20580.91861.17770.07010.03740.09570.375-0.12070.15790.1005-0.23780.03980.2223-0.00560.02150.2441-0.00450.1348-10.92880.147814.3095
41.34080.79851.12392.85861.64733.6290.0895-0.1225-0.0320.9099-0.19910.23150.1771-0.33310.0240.4473-0.08360.03880.28220.0240.1586-12.7561-4.15419.887
50.73510.2708-0.13652.92190.60252.72680.0851-0.04510.04680.1463-0.0479-0.1643-0.24290.04080.00420.201-0.0161-0.01350.16650.00020.1268-6.11296.395613.7099
60.5950.81690.1391.2033-0.25522.1361-0.16440.03560.0295-0.77490.3772-0.6388-1.14140.7147-0.12220.6674-0.29710.230.428-0.0270.38454.098111.3685-9.2135
70.9020.8574-0.06311.9026-0.60310.8722-0.02730.1068-0.1197-0.65490.1944-0.7797-0.60810.93150.02350.4125-0.18610.25620.5593-0.09740.42717.61714.3922-9.8504
80.7911-0.0566-0.08181.08880.17020.49140.05010.1238-0.0523-1.0490.1013-0.2263-0.87650.38190.00690.5343-0.08690.10460.23880.01870.1453-3.92193.3539-12.1827
90.3734-0.2980.38433.48351.05641.04050.0624-0.0312-0.0726-0.7114-0.26150.3542-0.361-0.24420.12090.34160.0576-0.09080.3102-0.03040.2012-17.1498-1.6189-11.9646
100.9933-0.213-0.37871.75521.72314.3421-0.21460.274-0.0295-0.86390.02870.1389-0.1009-0.1641-0.02870.77630.00650.01960.2949-0.0010.1089-12.08952.0998-19.5411
110.3469-0.2849-0.46292.29561.06695.2437-0.06530.0506-0.0287-0.17330.1056-0.09870.5928-0.1265-0.04840.2509-0.0107-0.00370.2207-0.00120.1859-12.1043-13.8316-7.9806
121.4955-0.66520.81381.98770.68046.34610.3138-0.1496-0.24220.2950.03680.69290.9475-1.0566-0.0890.2769-0.0734-0.1080.3182-0.02020.3298-21.3705-17.5797-12.8183
131.41180.8226-0.36344.80420.08680.1353-0.00150.11950.1411-0.2363-0.09360.0716-0.6071-0.0623-0.07790.4090.0215-0.00970.24430.01720.154-11.5637-0.4453-12.9469
141.02310.00330.27040.9305-0.45581.65340.10070.0392-0.15550.0320.0329-0.284-0.23940.1616-0.1130.42160.01850.03210.2005-0.01010.1697-6.5676-11.8206-13.5295
152.34781.5553-0.85421.0579-0.78051.86340.12340.2391-0.0659-0.66150.1045-0.6524-0.37110.7508-0.08690.6043-0.03810.25260.4476-0.13410.39774.6527-6.5897-21.203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 62 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 112 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 154 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 179 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 294 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 60 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 61 through 94 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 134 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 135 through 154 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 179 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 180 through 212 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 213 through 226 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 227 through 245 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 246 through 268 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 269 through 293 )B0

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