[English] 日本語
Yorodumi
- PDB-4txm: Crystal structure of uridine phosphorylase from Schistosoma manso... -

+
Open data


ID or keywords:

Loading...

-
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 phosphorylase / nucleotide catabolic process / UMP salvage / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more