[English] 日本語
Yorodumi
- PDB-1nyn: Solution NMR Structure of Protein YHR087W from Saccharomyces cere... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nyn
TitleSolution NMR Structure of Protein YHR087W from Saccharomyces cerevisiae. Northeast Structural Genomics Consortium Target YTYST425.
ComponentsHypothetical 12.0 kDa protein in NAM8-GAR1 intergenic region
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


RNA metabolic process / rRNA processing / nucleus / cytoplasm
Similarity search - Function
Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A; / Ribosome maturation protein SBDS, N-terminal domain / Ribosome maturation protein SDO1/SBDS, N-terminal / Ribosome maturation protein SBDS, N-terminal domain superfamily / Ribosome maturation protein Sdo1/SBDS-like / Shwachman-Bodian-Diamond syndrome (SBDS) protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Restriction of telomere capping protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsCort, J.R. / Yee, A.A. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.
Authors: Savchenko, A. / Krogan, N. / Cort, J.R. / Evdokimova, E. / Lew, J.M. / Yee, A.A. / Sanchez-Pulido, L. / Andrade, M.A. / Bochkarev, A. / Watson, J.D. / Kennedy, M.A. / Greenblatt, J. / ...Authors: Savchenko, A. / Krogan, N. / Cort, J.R. / Evdokimova, E. / Lew, J.M. / Yee, A.A. / Sanchez-Pulido, L. / Andrade, M.A. / Bochkarev, A. / Watson, J.D. / Kennedy, M.A. / Greenblatt, J. / Hughes, T. / Arrowsmith, C.H. / Rommens, J.M. / Edwards, A.M.
History
DepositionFeb 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical 12.0 kDa protein in NAM8-GAR1 intergenic region


Theoretical massNumber of molelcules
Total (without water)14,1951
Polymers14,1951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1combination of low energy, close to average, and few violations

-
Components

#1: Protein Hypothetical 12.0 kDa protein in NAM8-GAR1 intergenic region


Mass: 14194.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YHR087W / Plasmid: pET 15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38804

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1324D 13C-separated NOESY
141HNHA
NMR detailsText: BACKBONE AND SIDECHAIN ASSIGNMENTS WERE DETERMINED MANUALLY FROM TRIPLE-RESONANCE NMR DATA. NOE DISTANCE RESTRAINTS WERE DERIVED MANUALLY FROM NOESY DATA. PHI DIHEDRAL ANGLE RESTRAINTS WERE ...Text: BACKBONE AND SIDECHAIN ASSIGNMENTS WERE DETERMINED MANUALLY FROM TRIPLE-RESONANCE NMR DATA. NOE DISTANCE RESTRAINTS WERE DERIVED MANUALLY FROM NOESY DATA. PHI DIHEDRAL ANGLE RESTRAINTS WERE DERIVED FROM THE HNHA EXPERIMENT. PSI DIHEDRAL ANGLE RESTRAINTS WERE DERIVED FROM NOE RATIOS, SECONDARY STRUCTURE PROPENSITIES EVIDENT IN PRELIMINARY STRUCTURES, AND FROM ALPHA CARBON 13C CHEMICAL SHIFT TRENDS. RESIDUES 51-59 COMPRISE A POORLY-DEFINED LOOP IN THIS ENSEMBLE OF STRUCTURES. RESIDUES 92 TO 110 ARE ALSO NOT WELL-DEFINED IN THE ENSEMBLE.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM YHR087W U-13C,15N, 10mM Sodium Acetate, 300mM NaCl90% H2O/10% D2O
21mM YHR087W U-13C,15N, 10mM Sodium Acetate, 300mM NaCl100% D2O
Sample conditionsIonic strength: 300mM NaCl / pH: 5.0 / 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian UNITYVarianUNITY6003

-
Processing

NMR software
NameVersionDeveloperClassification
NIH-XPLOR2.0.4Brunger, A.T., Schwieters, C.D., Kuszewski, J.J., Tjandra, N., Clore, G.M.refinement
Felix97processing
NIH-XPLOR2.0.4Brunger, A.T., Schwieters, C.D., Kuszewski, J.J., Tjandra, N., Clore, G.M.structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 665 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE RESTRAINTS, 73 DIHEDRAL ANGLE RESTRAINTS, AND 44 HYDROGEN BOND RESTRAINTS (10.0 RESTRAINTS PER ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 665 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE RESTRAINTS, 73 DIHEDRAL ANGLE RESTRAINTS, AND 44 HYDROGEN BOND RESTRAINTS (10.0 RESTRAINTS PER RESIDUE FOR RESIDUES 4-90, EXCLUDING LOOP RESIDUES 51-59). THE 20 RESIDUE N-TERMINAL TAG (MGSSHHHHHHSSGLVPRGSH) WAS NOT INCLUDED IN THE STRUCTURE CALCULATION AND IS NOT PRESENT IN THE COORDINATES.
NMR representativeSelection criteria: combination of low energy, close to average, and few violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / 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://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