[English] 日本語
Yorodumi
- PDB-2lok: Solution NMR Structure of the uncharacterized protein from gene l... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lok
TitleSolution NMR Structure of the uncharacterized protein from gene locus VNG_0733H of Halobacterium salinarium, Northeast Structural Genomics Consortium Target HsR50
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homologyProtein of unknown function DUF1684 / Protein of unknown function (DUF1684) / DUF1684 family protein
Function and homology information
Biological speciesHalobacterium sp. NRC-1 (Halophile)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Lange, O.F. / Lee, H. / Hamilton, K. / Ciccosanti, C. / Buchwald, W.A. / Wang, H. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Rossi, P. / Lange, O.F. / Lee, H. / Hamilton, K. / Ciccosanti, C. / Buchwald, W.A. / Wang, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.
Authors: Lange, O.F. / Rossi, P. / Sgourakis, N.G. / Song, Y. / Lee, H.W. / Aramini, J.M. / Ertekin, A. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D.
History
DepositionJan 24, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,5821
Polymers21,5821
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein


Mass: 21582.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium sp. NRC-1 (Halophile) / Strain: ATCC 700922 / JCM 11081 / NRC-1 / Gene: VNG_0733H / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HRE7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
172cCH NOESY
182nNH NOESY
1913D HNHA
11013D 1H-13C NOESY
11113D (H)CCH-TOCSY
11223D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic
11513D 1H-15N NOESY
11623D 1H-15N NOESY
11732D 1H-15N HSQC
11813D HA(CO)NH

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.726 mM [U-100% 13C; U-100% 15N] hsr50.005, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
20.800 mM [U-100% 13C; U-100% 15N;U-2H] hsr50.009, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
30.674 mM [U-100% 13C; U-100% 15N] hsr50.007, 1 x Proteinase Inhibitors, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 200 mM NaCL, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.726 mMhsr50.005-1[U-100% 13C; U-100% 15N]1
1 %Proteinase Inhibitors-21
0.02 %NaN3-31
10 mMDTT-41
5 mMCaCL2-51
200 mMNaCL-61
20 mMMES pH 6.5-71
10 %D2O-81
50 uMDSS-91
0.800 mMhsr50.009-10[U-100% 13C; U-100% 15N;U-2H]2
1 %Proteinase Inhibitors-112
0.02 %NaN3-122
10 mMDTT-132
5 mMCaCL2-142
200 mMNaCL-152
20 mMMES pH 6.5-162
10 %D2O-172
50 uMDSS-182
0.674 mMhsr50.007-19[U-100% 13C; U-100% 15N]3
1 %Proteinase Inhibitors-203
0.02 %NaN3-213
10 mMDTT-223
5 mMCaCL2-233
200 mMNaCL-243
20 mMMES pH 6.5-253
10 %D2O-263
50 uMDSS-273
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
PSVSBhattacharya, Montelionestructure validation
PdbStat5.5-expTejero; Montelionestructure validation
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: cns 1.3 with RDC, noe, dihedral and h-bonds constraints using PARAM19 force field.
NMR constraintsNOE constraints total: 3047
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
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