[English] 日本語
Yorodumi
- PDB-5gjl: Solution structure of SUMO from Plasmodium falciparum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gjl
TitleSolution structure of SUMO from Plasmodium falciparum
ComponentsUncharacterized protein
KeywordsPROTEIN BINDING / SUMO
Function / homologyRad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Ubiquitin-like domain-containing protein
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / molecular dynamics
AuthorsSingh, J.S. / Shukla, V.K. / Gujrati, M. / Mishra, R.K. / Kumar, A.
CitationJournal: To Be Published
Title: Structure, dynamics and interaction study of SUMO from Plasmodium falciparum
Authors: Singh, J.S. / Shukla, V.K. / Gujrati, M. / Mishra, R.K. / Kumar, A.
History
DepositionJun 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,8391
Polymers10,8391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein / PfSUMO


Mass: 10838.997 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate Dd2) (eukaryote)
Strain: isolate Dd2 / Gene: PFDG_04583 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L7M5F7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic13D CBCA(CO)NH
132isotropic13D HN(CA)CB
142isotropic13D HNCO
152isotropic13D (H)CCH-TOCSY
162isotropic13D (H)CC(CO)NH
172isotropic13D CC(CO)NH
181isotropic23D 1H-15N NOESY
193isotropic23D 1H-13C NOESY aliphatic
1102isotropic12D 1H-13C HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O15N90% H2O/10% D2O
solution220 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O15N, 13C90% H2O/10% D2O
solution320 mM TRIS, 50 mM sodium chloride, 100% D2O15N, 13C100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRISnatural abundance1
50 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance2
50 mMsodium chloridenatural abundance2
20 mMTRISnatural abundance3
50 mMsodium chloridenatural abundance3
Sample conditionsIonic strength: 50 mM / Ionic strength err: 0.2 / Label: sample condition 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.2

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ASCENDBrukerASCEND7501
Bruker AVANCEBrukerAVANCE7002

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CcpNMRCCPNchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: 1329 NOE and 136 dihedral angle
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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