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

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Basic information

Entry
Database: PDB / ID: 4txn
TitleCrystal structure of uridine phosphorylase from Schistosoma mansoni in complex with 5-fluorouracil
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
5-FLUOROURACIL / Uridine phosphorylase A
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _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
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,50312
Polymers130,5984
Non-polymers9058
Water23,2571291
1
A: Uridine phosphorylase
B: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7516
Polymers65,2992
Non-polymers4524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-67 kcal/mol
Surface area19920 Å2
MethodPISA
2
C: Uridine phosphorylase
D: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7516
Polymers65,2992
Non-polymers4524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-68 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.643, 107.488, 115.576
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.: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Comment: medication, chemotherapy*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1291 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200mM ammonium sulphate, 100mM Bis-tris pH 5.5, 20-25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 80105 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge F obs: 0.177 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.114 / Χ2: 0.928 / Net I/σ(I): 11.61 / Num. measured all: 306780
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
2-2.120.6840.5392.414445412909121900.6394.4
2.12-2.260.4510.3643.714592412171120790.42499.2
2.26-2.440.3260.2695.074360411368112940.31299.3
2.44-2.680.2340.1936.994082710508104500.22499.4
2.68-2.990.1530.12910.2337214952894960.1599.7
2.99-3.440.0820.07616.8232981845584250.08899.6
3.44-4.20.0470.04726.2727791720671650.05499.4
4.2-5.880.0340.03631.121618567756370.04299.3
5.880.0230.02736.6612367343133690.03198.2

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TXJ
Resolution: 2→29.016 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 4005 5 %Random selection
Rwork0.1715 76074 --
obs0.1732 80079 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.25 Å2 / Biso mean: 22.385 Å2 / Biso min: 7 Å2
Refinement stepCycle: final / Resolution: 2→29.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8648 0 56 1291 9995
Biso mean--15.3 33.16 -
Num. residues----1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048889
X-RAY DIFFRACTIONf_angle_d0.86512048
X-RAY DIFFRACTIONf_chiral_restr0.0321408
X-RAY DIFFRACTIONf_plane_restr0.0031547
X-RAY DIFFRACTIONf_dihedral_angle_d11.6033084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02150.27081070.23512017X-RAY DIFFRACTION78
2.0215-2.04610.24411350.21032568X-RAY DIFFRACTION99
2.0461-2.0720.24931380.20742625X-RAY DIFFRACTION99
2.072-2.09930.24821370.19822598X-RAY DIFFRACTION99
2.0993-2.1280.20631370.19372616X-RAY DIFFRACTION99
2.128-2.15840.24741370.19332594X-RAY DIFFRACTION99
2.1584-2.19060.25681370.18062607X-RAY DIFFRACTION99
2.1906-2.22480.22571390.17742640X-RAY DIFFRACTION99
2.2248-2.26130.22011360.17852591X-RAY DIFFRACTION99
2.2613-2.30030.23591380.17472615X-RAY DIFFRACTION99
2.3003-2.34210.23331390.17142645X-RAY DIFFRACTION99
2.3421-2.38710.2261390.16912637X-RAY DIFFRACTION99
2.3871-2.43580.21251370.16512603X-RAY DIFFRACTION99
2.4358-2.48870.21361370.17192611X-RAY DIFFRACTION99
2.4887-2.54660.21011390.16372629X-RAY DIFFRACTION99
2.5466-2.61020.21251380.17732626X-RAY DIFFRACTION100
2.6102-2.68080.2331400.17582665X-RAY DIFFRACTION99
2.6808-2.75960.21711390.17332632X-RAY DIFFRACTION99
2.7596-2.84860.22461380.1812632X-RAY DIFFRACTION100
2.8486-2.95030.21331410.17212660X-RAY DIFFRACTION100
2.9503-3.06830.19461400.16872660X-RAY DIFFRACTION100
3.0683-3.20780.20291380.1672640X-RAY DIFFRACTION99
3.2078-3.37670.19491400.16782651X-RAY DIFFRACTION100
3.3767-3.58790.17491420.15572691X-RAY DIFFRACTION100
3.5879-3.86430.19461410.14942677X-RAY DIFFRACTION100
3.8643-4.25210.18521400.14672669X-RAY DIFFRACTION99
4.2521-4.86490.15081420.14282697X-RAY DIFFRACTION99
4.8649-6.11980.22721440.17682727X-RAY DIFFRACTION99
6.1198-29.01910.19951500.19332851X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.119-0.35190.36141.4922-0.74021.57850.02250.0432-0.113-0.22490.12250.19780.2099-0.1618-0.11560.1799-0.0332-0.02110.163-0.00470.1617-35.61220.3958-14.7125
22.22820.09240.68411.58980.38852.40880.1083-0.2096-0.1494-0.10740.08760.47760.1516-0.4462-0.14320.1923-0.0416-0.07090.19140.03030.244-43.10823.7128-12.0002
30.6296-0.1417-0.1951.2616-0.33650.93410.01770.01710.0373-0.23350.00810.0180.06980.0891-0.04580.1998-0.00910.010.1508-0.00590.1138-26.409612.6404-17.0934
41.54030.51190.53861.95440.43663.4685-0.1790.34750.107-0.33290.16710.2334-0.1903-0.0542-0.05420.2706-0.036-0.0020.18520.04090.1619-33.339722.7985-29.7015
50.93360.0869-0.12491.57760.11722.80430.0634-0.06550.14770.05370.0337-0.1223-0.60030.4284-0.08590.2834-0.0560.02680.1891-0.02340.1873-22.705932.7351-8.2574
60.7174-0.1354-0.02371.5609-0.29421.21450.08580.01170.0263-0.0606-0.06420.00750.10250.0964-0.07750.1987-0.01810.00070.155-0.00110.1367-25.744516.7782-19.6737
70.9124-0.30080.1551.13710.14191.6860.20450.16760.1884-0.0201-0.02950.1523-0.2486-0.3188-0.13480.2387-0.00670.04030.21870.02930.2069-38.267330.906-12.6563
80.85690.44160.0692.770.46471.57220.08320.3111-0.0751-0.36240.11110.21630.1182-0.1397-0.1070.2822-0.011-0.09710.24950.04830.2065-42.571112.6035-29.3715
91.28450.33570.02662.203-0.62571.3840.0799-0.05020.1079-0.0185-0.00470.2503-0.2002-0.255-0.08640.19160.05050.04190.1965-0.02210.1959-39.475123.97657.0926
100.60020.03620.16061.3621-0.03370.6702-0.0087-0.00450.08830.09950.0582-0.0384-0.14140.1347-0.07780.1653-0.01540.0190.1779-0.03180.1304-25.518518.17847.4176
111.7892-0.6726-0.87191.93741.13294.059-0.193-0.3103-0.08640.49640.1524-0.00950.3201-0.12710.1050.23360.0424-0.01510.2871-0.01690.1263-24.13986.510320.7415
120.5003-0.24-0.23491.18860.33020.97040.0844-0.05820.0112-0.0239-0.0288-0.1258-0.05320.1357-0.06220.13720.00790.00260.174-0.01890.1374-19.39295.11352.7866
131.5343-1.5031-1.02734.76442.91384.22860.0295-0.22190.01740.38760.0602-0.0665-0.0250.0251-0.01230.1883-0.02530.03120.2064-0.00330.1171-35.57627.195317.3977
143.2927-0.8969-1.60273.81161.09883.9505-0.0824-0.17570.21670.5625-0.10460.20050.1346-0.2930.15850.1529-0.0141-0.01960.1774-0.00460.2144-89.9821-17.600616.2412
150.7446-0.15370.13150.75130.00670.6061-0.0243-0.05960.03760.06830.03110.02770.0514-0.0057-0.00230.137-0.01970.00470.131-0.02520.1069-72.2891-20.21614.7601
161.8804-0.31350.41972.1825-0.97742.98840.0302-0.29690.03450.1777-0.0688-0.27660.25440.19510.00990.1902-0.0335-0.02120.2048-0.0310.175-54.2519-19.055320.8228
170.63940.0587-0.07630.8141-0.30681.16910.0371-0.01940.07660.0492-0.0547-0.0538-0.09950.12270.02570.0984-0.0119-0.00560.1352-0.01930.1322-59.8707-14.14058.961
183.47191.2315-0.83484.8229-0.96673.4582-0.11620.37120.117-0.4324-0.0652-0.4003-0.17780.5980.11910.1878-0.03370.00310.24720.0020.218-57.7847-12.3746-11.5083
191.61190.17990.57771.1409-0.18851.7152-0.10770.3487-0.1446-0.19060.0679-0.09010.03310.21620.07280.1751-0.00990.03120.1468-0.02270.1544-67.5512-19.1936-18.0527
202.29070.72320.65221.80880.5572.7809-0.00110.1119-0.35380.05440.0262-0.00670.3631-0.0177-0.08090.15280.02430.03270.1002-0.01380.1722-75.9734-26.6845-13.0984
210.7403-0.0338-0.13830.79390.3220.84110.02970.05410.0824-0.1035-0.0441-0.0228-0.0274-0.03130.02470.13590.00450.00280.11640.00330.1294-77.8071-12.039-10.5309
222.12530.01150.24950.7626-0.02040.1690.0424-0.06420.32560.1246-0.10240.0357-0.1212-0.00130.06820.20880.0046-0.00260.119-0.0140.2052-75.09092.3272-3.1406
231.3133-0.3202-0.15761.11990.02032.93850.06070.3131-0.0054-0.24550.04640.41880.2025-0.26790.02530.15250.0397-0.05660.2086-0.00660.2457-93.2883-10.2606-15.2837
240.8977-0.2746-0.28190.4151-0.54832.2833-0.1357-0.08280.0650.16670.09220.0553-0.3188-0.09770.02610.14860.0238-0.01210.161-0.03410.1956-89.3378-4.4249.4962
253.1823-0.4515-1.28430.59510.63591.3237-0.0923-0.08880.0833-0.02460.0578-0.02540.00950.06080.04160.12580.0037-0.0180.0991-0.0040.1388-80.1643-4.9081-6.6744
260.47690.1223-0.14710.5606-0.10320.8832-0.0096-0.07620.0062-0.0952-0.05040.1314-0.0012-0.10610.05510.11660.0105-0.01440.1401-0.02690.1615-89.6664-12.3125-2.223
272.224-0.3914-1.55030.9989-0.16033.791-0.03670.1978-0.0877-0.2943-0.00740.07660.1723-0.2770.04370.1747-0.0307-0.02390.1718-0.04020.1576-88.3392-21.1027-15.8109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 61 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 83 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 166 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 193 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 225 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 255 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 256 through 277 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 296 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 79 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 166 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 167 through 193 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 194 through 268 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 269 through 295 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 7 through 24 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 25 through 166 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 167 through 193 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 194 through 296 )C0
18X-RAY DIFFRACTION18chain 'D' and (resid 7 through 24 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 25 through 47 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 48 through 83 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 84 through 142 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 143 through 166 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 167 through 193 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 194 through 226 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 227 through 245 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 246 through 268 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 269 through 296 )D0

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