[English] 日本語
Yorodumi
- PDB-1n6z: Solution NMR Structure of Protein YML108W from Saccharomyces cere... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n6z
TitleSolution NMR Structure of Protein YML108W from Saccharomyces cerevisiae. A novel member of the split bab fold. Northeast Structural Genomics Consortium Target YT601.
ComponentsHypothetical 12.3 kDa protein in ZDS2-URA5 intergenic region
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / STRUCTURAL PROTEOMICS / OCSP / NESG / PROTEIN STRUCTURE INITIATIVE / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


nucleus / cytoplasm
Similarity search - Function
YML108W-like / Protein of unknown function DUF1892 / YML108W-like superfamily / Protein of unknown function (DUF1892) / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YML108W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPineda-Lucena, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: PROTEIN SCI. / Year: 2003
Title: A novel member of the split beta-alpha-beta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae. Ontario Centre for Structural Proteomics target (YST0204_ ...Title: A novel member of the split beta-alpha-beta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae. Ontario Centre for Structural Proteomics target (YST0204_1_105); Northeast Structural Genomics Target (YT601).
Authors: Pineda-Lucena, A. / Liao, J.C.C. / Cort, J.R. / Yee, A. / Kennedy, M.A. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionNov 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999 The protein that was structurally determined also contains a His tag prior to the sequence listed ... The protein that was structurally determined also contains a His tag prior to the sequence listed in the SEQRES. The His tag sequence is MGSSHHHHHHSSGLVPRGSH. These His tag residues were missing in the electron density.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical 12.3 kDa protein in ZDS2-URA5 intergenic region


Theoretical massNumber of molelcules
Total (without water)12,3551
Polymers12,3551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Hypothetical 12.3 kDa protein in ZDS2-URA5 intergenic region


Mass: 12355.082 Da / Num. of mol.: 1 / Fragment: YML108W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YML108W OR YM8339.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03759

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D HETERONUECLEAR NMR TECHNIQUES

-
Sample preparation

DetailsContents: 1 mM, U-15N,13C 25 mM sodium phosphate (pH=6.5), 450 mM NaCl, 1 mM DTT
Solvent system: 95% H20/5% D2O
Sample conditionsIonic strength: 0.9 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1DELAGLIO ET AL.processing
DYANA1.5GUNTERT ET AL.structure solution
XEASY1.3.14BARTELS ET AL.data analysis
CYANA1.0.5HERRMANN ET AL.structure solution
DYANA1.5GUNTERT ET AL.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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