[English] 日本語
Yorodumi
- PDB-6ns8: RDC-refined SOLUTION NMR STRUCTURE OF PROTEIN PF2048.1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ns8
TitleRDC-refined SOLUTION NMR STRUCTURE OF PROTEIN PF2048.1
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION
Function / homologyPCRF domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsDaigham, N.S. / Liu, G. / Swapna, G.V.T. / Cole, C. / Valafar, H. / Montelione, G.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: REDCRAFT: A Computational Platform Using Residual Dipolar Coupling NMR Data for Determining Structures of Perdeuterated Proteins Without NOEs
Authors: Daigham, N.S. / Liu, G. / Swapna, G.V.T. / Cole, C. / Valafar, H. / Montelione, G.T.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Experimental preparation / Structure summary
Category: citation / pdbx_nmr_details / struct / Item: _citation.title / _struct.title
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)9,3531
Polymers9,3531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

-
Components

#1: Protein Uncharacterized protein


Mass: 9352.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus COM1 (archaea) / Gene: PFC_08315 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I6V394

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic
Type: 3D SIMULTANEOUS 13C-AROMATIC,13C-ALIPHATIC,15N EDITED 1H-1H NOESY
NMR detailsText: The authors state that the medoid structure is conformer model 13

-
Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] PF2048.1, 90% H2O/10% D2O
Details: 0.8 MM [U-100% 13C; U-100% 15N] PF2048.1, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 NA CALCIUM CHLORIDE, 0.02 % SODIUM AZIDE, 10 % DSS, 90% H2O/10% D2O
Label: NC / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: PF2048.1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: NC / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
SparkyGoddardpeak picking
AutoStructureHuang, Tejero, Powers and Montelionerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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