[English] 日本語
Yorodumi
- PDB-5ko6: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ko6
TitleCrystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with cytosine and ribose-1-phosphate
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
6-AMINOPYRIMIDIN-2(1H)-ONE / 1-O-phosphono-alpha-D-ribofuranose / Purine nucleoside phosphorylase / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsTorini, J.R. / Romanello, L. / Bird, L. / Owens, R. / 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
DepositionJun 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 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 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)31,7013
Polymers31,3591
Non-polymers3412
Water6,197344
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)95,1029
Polymers94,0783
Non-polymers1,0246
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9830 Å2
ΔGint-58 kcal/mol
Surface area30340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.640, 98.640, 98.640
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-626-

HOH

21A-671-

HOH

31A-725-

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) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U3AGT1, UniProt: G4VP83*PLUS, purine-nucleoside phosphorylase
#2: Chemical ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O
#3: Sugar ChemComp-R1P / 1-O-phosphono-alpha-D-ribofuranose / RIBOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-ribose / 1-O-phosphono-D-ribose / 1-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Lithium chloride, 0.1 M Cadmium chloride hemi(pentahydrate), 0.1 M Sodium acetate 4.5 30 % v/v PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.42→44.113 Å / Num. obs: 60417 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.42-1.469.11.6070.541100
6.35-44.1110.60.037199.2

-
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: 1CXQ

1cxq


Resolution: 1.42→44.113 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.39
RfactorNum. reflection% reflection
Rfree0.1785 2943 4.87 %
Rwork0.1619 --
obs0.1627 60379 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.42 Å2 / Biso mean: 25.063 Å2 / Biso min: 9.22 Å2
Refinement stepCycle: final / Resolution: 1.42→44.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 22 344 2544
Biso mean--32.56 35.99 -
Num. residues----285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062245
X-RAY DIFFRACTIONf_angle_d0.9533049
X-RAY DIFFRACTIONf_chiral_restr0.084357
X-RAY DIFFRACTIONf_plane_restr0.006394
X-RAY DIFFRACTIONf_dihedral_angle_d18.599833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4201-1.44330.2651240.296927062830
1.4433-1.46820.31521540.279927452899
1.4682-1.49490.30011340.252226942828
1.4949-1.52370.261380.226326812819
1.5237-1.55480.22121350.210726962831
1.5548-1.58860.21491560.206627442900
1.5886-1.62550.20391240.193827052829
1.6255-1.66620.19651390.184427502889
1.6662-1.71120.20611450.178126802825
1.7112-1.76160.21271500.177327222872
1.7616-1.81850.19691360.172727042840
1.8185-1.88350.19861520.167127322884
1.8835-1.95890.17331400.160727192859
1.9589-2.0480.18361430.160127402883
2.048-2.1560.15781290.150327202849
2.156-2.29110.1731240.151827742898
2.2911-2.4680.16251470.156527382885
2.468-2.71630.16511390.156327512890
2.7163-3.10920.18181410.151227672908
3.1092-3.91690.17231490.145127772926
3.9169-44.13440.14581440.147428913035
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)
16.6929-4.16392.69182.7813-1.37293.9980.08380.249-0.6618-0.1626-0.04160.45290.3933-0.3230.00890.1938-0.02230.07030.1654-0.02540.2363-27.6444-36.6056-4.7268
22.14220.53270.89412.46290.47552.9110.0951-0.1514-0.56870.2148-0.0726-0.04290.58920.1709-0.02760.27210.06950.03380.16870.04940.2788-12.0863-41.48392.721
31.8372-0.0322-0.43591.5097-0.77921.9061-0.0116-0.0346-0.27780.0841-0.02970.00250.13180.07920.03380.14540.01610.02270.1040.00120.1761-15.5933-34.2473-3.8423
41.9108-0.50620.17751.1057-0.18570.612-0.0856-0.17660.00840.19410.0563-0.0289-0.00230.03540.03020.13970.02410.00720.1086-0.00130.07-11.5368-19.62532.5781
51.01830.22270.41732.0218-1.45563.2853-0.0773-0.2875-0.02340.52310.0419-0.1746-0.13280.05390.02590.2750.0855-0.03330.23060.00010.1102-1.4893-23.945914.5877
61.90630.1887-0.12240.9138-0.48490.7272-0.0187-0.04920.06170.1177-0.0414-0.1062-0.06290.11190.06570.15190.0212-0.01250.14060.0090.1221-1.2432-18.2577-1.8766
74.69861.9682-4.43683.409-2.59036.0606-0.0580.0231-0.06910.17040.1830.09770.1839-0.2584-0.01460.20280.0878-0.06330.21280.04230.1633-0.3499-33.56338.1842
81.9999-2.51569.66492.0005-8.96364.1627-0.8959-2.8825-0.5927-0.01010.4130.06780.006-0.62960.49330.46910.6055-0.28120.82180.03490.07822.098-22.3631-4.697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 22 )A3 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 54 )A23 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 108 )A55 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 169 )A109 - 169
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 196 )A170 - 196
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 258 )A197 - 258
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 287 )A259 - 287
8X-RAY DIFFRACTION8chain 'A' and (resid 301 through 301 )A301

+
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