[English] 日本語
Yorodumi
- PDB-2kyi: Solution NMR structure of Dsy0195(21-82) protein from Desulfitoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kyi
TitleSolution NMR structure of Dsy0195(21-82) protein from Desulfitobacterium Hafniense. Northeast Structural Genomics Consortium Target DhR8C
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / YabP family / Desulfitobacterium Hafniense / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore
Similarity search - Function
Immunoglobulin-like - #2000 / Spore protein YabP / Spore protein YabP/YqfC / YabP superfamily / YabP family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sporulation protein YabP
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Cort, J.R. / Wang, H. / Ciccosanti, C. / Foote, E.L. / Jiang, M. / Janjua, H. / Acton, T.B. / Xiao, R. ...Yang, Y. / Ramelot, T.A. / Cort, J.R. / Wang, H. / Ciccosanti, C. / Foote, E.L. / Jiang, M. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Combining NMR and EPR methods for homodimer protein structure determination.
Authors: Yang, Y. / Ramelot, T.A. / McCarrick, R.M. / Ni, S. / Feldmann, E.A. / Cort, J.R. / Wang, H. / Ciccosanti, C. / Jiang, M. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionMay 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,0042
Polymers16,0042
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 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein


Mass: 8002.207 Da / Num. of mol.: 2 / Fragment: sequence database residues 21-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: Y51 / Gene: DSY0195 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q251Q8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC CT
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D HN(CO)CA
11113D HBHA(CO)NH
11213D H(CCO)NH
11313D C(CO)NH
11413D (H)CCH-TOCSY
11513D (H)CCH-COSY
11633D (H)CCH-TOCSY
11734D CC NOESY
11812D 1H-15N HSQC Histidine
11912D 1H-15N HSQC swN150ppm

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] Dsy0195(21-82) protein from Desulfitobacterium Hafniense, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-5% 13C; U-100% 15N] Dsy0195(21-82) protein from Desulfitobacterium Hafniense, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] Dsy0195(21-82) protein from Desulfitobacterium Hafniense, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMDsy0195(21-82) protein from Desulfitobacterium Hafniense-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
1 mMDsy0195(21-82) protein from Desulfitobacterium Hafniense-7[U-5% 13C; U-100% 15N]2
20 mMammonium acetate-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
1.0 mMDsy0195(21-82) protein from Desulfitobacterium Hafniense-13[U-100% 13C; U-100% 15N]3
20 mMammonium acetate-143
200 mMsodium chloride-153
5 mMcalcium chloride-163
10 mMDTT-173
0.02 %sodium azide-183
1.0 mMDsy0195(21-82) protein from Desulfitobacterium Hafniense-19[U-100% 13C; U-100% 15N]4
20 mMammonium acetate-204
200 mMsodium chloride-214
5 mMcalcium chloride-224
10 mMDTT-234
0.02 %sodium azide-244
Sample conditionsIonic strength: 0.2 / pH: 4.5 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
CYANA2.1.3Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1.3Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-nih-2.20 with HBDB
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / 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