[English] 日本語
Yorodumi
- PDB-2kvt: solution NMR structure of yaiA from Escherichia Eoli. Northeast S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kvt
Titlesolution NMR structure of yaiA from Escherichia Eoli. Northeast Structural Genomics Target ER244
ComponentsUncharacterized protein yaiA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / yaiA / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYaiA protein / YaiA protein / YaiA-like superfamily / YaiA protein / GCC-box Binding Domain / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YaiA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsTang, Y. / Chen, X. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Everett, J. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: solution NMR structure of yaiA from Escherichia coli. Northeast Structural Genomics Target ER244
Authors: Tang, Y. / Chen, X. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Everett, J. / Montelione, G.T.
History
DepositionMar 28, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: pdbx_database_status / pdbx_nmr_sample_details ...pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _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
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein yaiA


Theoretical massNumber of molelcules
Total (without water)8,3641
Polymers8,3641
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein yaiA


Mass: 8364.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yaiA, b0389, JW0380 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AAN5

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HN(CA)CB
1523D CBCA(CO)NH
1623D HNCA
1723D (H)CCH-TOCSY
1823D (H)CCH-COSY
1923D CCH-TOCSY
11023D 1H-15N NOESY
11123D 1H-13C aliphatic NOESY
11223D 1H-13C aromatic NOESY
11312D 1H-13C HSQC (high resolution)

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.00 mM [U-5% 13C; U-100% 15N] ER244-1, 5 mM DTT-2, 100 mM sodium chloride-3, 10 mM TRIS-4, 10 mM NaN3-5, 95% H2O/5% D2O95% H2O/5% D2O
21.37 mM [U-100% 13C; U-100% 15N] ER244-6, 5 mM DTT-7, 100 mM sodium chloride-8, 10 mM TRIS-9, 10 mM NaN3-10, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.00 mMER244-1[U-5% 13C; U-100% 15N]1
5 mMDTT-21
100 mMsodium chloride-31
10 mMTRIS-41
10 mMNaN3-51
1.37 mMER244-6[U-100% 13C; U-100% 15N]2
5 mMDTT-72
100 mMsodium chloride-82
10 mMTRIS-92
10 mMNaN3-102
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
Sparky3.11Goddardpeak picking
Sparky3.11Goddarddata analysis
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA3.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.4Bhattacharya and Montelionestructure validation
RefinementMethod: simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
Software ordinal: 1
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://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