[English] 日本語
Yorodumi
- PDB-5tbu: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tbu
TitleCrystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Hypoxanthine
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE
Function / homology
Function and homology information


nucleoside metabolic process / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HYPOXANTHINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsFaheem, M. / Torini, J.R. / Romanello, L. / Brandao-Neto, J. / Pereira, H.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 Brazil
CitationJournal: PLoS ONE / Year: 2018
Title: The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs.
Authors: Torini, J.R. / Romanello, L. / Batista, F.A.H. / Serrao, V.H.B. / Faheem, M. / Zeraik, A.E. / Bird, L. / Nettleship, J. / Reddivari, Y. / Owens, R. / DeMarco, R. / Borges, J.C. / Brandao-Neto, J. / Pereira, H.D.
History
DepositionSep 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7305
Polymers31,3591
Non-polymers3714
Water4,071226
1
A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,19015
Polymers94,0783
Non-polymers1,11212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area10970 Å2
ΔGint-12 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.708, 99.708, 99.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-611-

HOH

-
Components

#1: Protein Purine nucleoside phosphorylase / Inosine-guanosine phosphorylase


Mass: 31359.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo
References: UniProt: A0A0U3AGT1, purine-nucleoside phosphorylase
#2: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium acetate, 0.1M Bis-Tris pH 6.5, 30% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→57.566 Å / Num. obs: 19582 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.92 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.164.70.851199.1
8.91-70.57.70.0441100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
xia2data scaling
xia2data reduction
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CXS

5cxs


Resolution: 2.1→57.566 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 902 4.61 %Random selection
Rwork0.1887 ---
obs0.1904 19553 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.33 Å2 / Biso mean: 25.2581 Å2 / Biso min: 8.61 Å2
Refinement stepCycle: final / Resolution: 2.1→57.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 22 226 2412
Biso mean--19.98 31.86 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022228
X-RAY DIFFRACTIONf_angle_d0.5243021
X-RAY DIFFRACTIONf_chiral_restr0.046351
X-RAY DIFFRACTIONf_plane_restr0.004391
X-RAY DIFFRACTIONf_dihedral_angle_d13.1051343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1002-2.23170.29071580.24713059321799
2.2317-2.40410.26261580.215130533211100
2.4041-2.6460.21261550.205430813236100
2.646-3.02890.2351500.195430923242100
3.0289-3.81590.22571560.17731143270100
3.8159-57.5880.19421250.162632523377100
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)
12.6005-1.56870.48815.27430.51232.5345-0.13810.01020.7364-0.37440.1282-0.5282-0.51160.2658-0.00850.2486-0.05180.00490.19160.00090.314427.5501-12.5202-3.2154
21.826-0.3902-0.72251.2968-0.89031.61280.0631-0.15140.6838-0.084-0.08730.0894-0.5326-0.14730.00610.33510.0158-0.05780.2047-0.07310.399911.3371-8.31582.9977
31.19640.1017-0.31921.00870.00921.2278-0.0310.03860.2773-0.1842-0.05880.2158-0.4012-0.12560.06070.29140.0149-0.05210.1944-0.03190.361313.8432-10.8399-2.0397
42.71191.31422.44890.66331.13522.31280.0378-0.11180.26960.0535-0.06480.20020.0764-0.1294-0.00870.1743-0.0045-0.01890.1525-0.01040.209916.4664-20.7697-5.2135
50.93170.08570.09830.6950.41230.5482-0.0249-0.14370.03450.09780.03080.06050.0325-0.0353-0.00390.13590.0115-0.00790.156-0.00290.133511.7532-30.20992.9606
60.99310.326-0.20791.59431.292.21290.1102-0.25390.03910.265-0.19320.14380.0693-0.39860.06040.19820.04580.02280.2905-0.00730.1730.7791-25.869714.898
70.95050.09350.00690.61480.33810.57810.0103-0.0257-0.05550.0249-0.06750.09510.0565-0.10970.05960.13060.00010.01320.1598-0.00960.14880.6877-31.7529-1.7588
81.44820.81821.47951.12110.83913.9708-0.1418-0.24710.35380.071-0.09520.0307-0.2274-0.25590.21280.18490.06070.02250.2172-0.05860.20830.167-16.2068.6364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 22 )A5 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 54 )A23 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 84 )A55 - 84
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 108 )A85 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 169 )A109 - 169
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 196 )A170 - 196
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 258 )A197 - 258
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 287 )A259 - 287

+
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://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