[English] 日本語
Yorodumi
- PDB-2ky9: Solution NMR Structure of ydhK C-terminal Domain from B.subtilis,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ky9
TitleSolution NMR Structure of ydhK C-terminal Domain from B.subtilis, Northeast Structural Genomics Consortium Target Target SR518
ComponentsUncharacterized protein ydhK
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / tandem tudor / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


SH3 type barrels. - #1130 / Thrombin, subunit H - #520 / Domain of unknown function DUF1541 / Protein of unknown function (DUF1541) / SH3 type barrels. / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein YdhK
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Sukumaran, D.K. / Lee, H. / Lee, D. / Ciccosanti, C. / Janjua, H. / Liu, J. / Rost, B. / Acton, T.B. / Xiao, R. ...Eletsky, A. / Sukumaran, D.K. / Lee, H. / Lee, D. / Ciccosanti, C. / Janjua, H. / Liu, J. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The copBL operon protects Staphylococcus aureus from copper toxicity: CopL is an extracellular membrane-associated copper-binding protein.
Authors: Rosario-Cruz, Z. / Eletsky, A. / Daigham, N.S. / Al-Tameemi, H. / Swapna, G.V.T. / Kahn, P.C. / Szyperski, T. / Montelione, G.T. / Boyd, J.M.
History
DepositionMay 21, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Revision 1.4May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein ydhK


Theoretical massNumber of molelcules
Total (without water)14,6111
Polymers14,6111
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)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein ydhK


Mass: 14611.321 Da / Num. of mol.: 1 / Fragment: sequence database residues 83-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU05790, ydhK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: O05503

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HN(CA)CO
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HBHA(CO)NH
1912D 1H-13C CT-HSQC aliphatic
11012D 1H-13C CT-HSQC aromatic
11113D (H)CCH-COSY aliphatic
11213D (H)CCH-TOCSY aliphatic
11313D (H)CCH-COSY aromatic
11422D 1H-13C CT-HSQC methyl
11522D 1H-15N LR-HSQC for Histidine
11622D 1H-15N J-MODULATED HSQC
11732D 1H-15N J-MODULATED HSQC
21842D 1H-15N J-MODULATED HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-5% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM [U-5% 13C; U-100% 15N] SR518, 100 mM sodium chloride, 5 mM DTT, 10 mM TRIS, 0.02 % sodium azide, 20 uM DSS, 3.5 % PEG, 88% H2O/12% D2O88% H2O/12% D2O
40.5 mM [U-5% 13C; U-100% 15N] SR518, 180 mM sodium chloride, 3.5 mM DTT, 7 mM TRIS, 0.014 % sodium azide, 14 uM DSS, 10.5 g/L Pf1 phage, 88% H2O/12% D2O88% H2O/12% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMSR518-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMDTT-31
10 mMTRIS-41
0.02 %sodium azide-51
20 uMDSS-61
0.7 mMSR518-7[U-5% 13C; U-100% 15N]2
100 mMsodium chloride-82
5 mMDTT-92
10 mMTRIS-102
0.02 %sodium azide-112
20 uMDSS-122
0.5 mMSR518-13[U-5% 13C; U-100% 15N]3
100 mMsodium chloride-143
5 mMDTT-153
10 mMTRIS-163
0.02 %sodium azide-173
20 uMDSS-183
3.5 %PEG-193
0.5 mMSR518-20[U-5% 13C; U-100% 15N]4
180 mMsodium chloride-214
3.5 mMDTT-224
7 mMTRIS-234
0.014 %sodium azide-244
14 uMDSS-254
10.5 g/LPf1 phage-264
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11007.5ambient 298 K
21807.5ambient 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503
Bruker AvanceBrukerAVANCE7004

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure calculation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
TopSpin2.1Bruker Biospincollection
VnmrJVariancollection
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
PROSA6.4Guntertprocessing
MOLMOL2K.2Koradi, Billeter and Wuthrichvisualization
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxdata analysis
PSVS1.3Bhattacharya and Montelionevalidation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak ...Details: Structure determination was performed by running CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments were selected and used in iterative refinement with CYANA, with RDC constraints added at later stages. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field and upper limit constraints relaxed by 5%
NMR constraintsNOE constraints total: 1797 / NOE intraresidue total count: 302 / NOE long range total count: 853 / NOE medium range total count: 258 / NOE sequential total count: 384 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 106 / Protein psi angle constraints total count: 106
NMR representativeSelection criteria: lowest energy
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://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