[English] 日本語
Yorodumi
- PDB-2m47: Solution NMR structure of the Polyketide_cyc-like protein Cgl2372... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m47
TitleSolution NMR structure of the Polyketide_cyc-like protein Cgl2372 from Corynebacterium glutamicum, Northeast Structural Genomics Consortium Target CgR160
ComponentsUncharacterized protein Cgl2373
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsYang, Y. / Ramelot, T.A. / Lee, D. / Ciccosanti, C. / Sapin, A. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Yang, Y. / Ramelot, T.A. / Lee, D. / Ciccosanti, C. / Sapin, A. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the Polyketide_cyc-like protein Cgl2372 from Corynebacterium glutamicum, Northeast Structural Genomics Consortium Target CgR160.
Authors: Yang, Y. / Ramelot, T.A. / Lee, D. / Ciccosanti, C. / Sapin, A. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJan 30, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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 Cgl2373


Theoretical massNumber of molelcules
Total (without water)18,8091
Polymers18,8091
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 Cgl2373


Mass: 18809.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: cg2606, Cgl2373 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8NN40

-
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
1713D 1H-13C NOESY aliphatic
1813D HNCA
1913D HN(CO)CA
11013D (H)CCH-TOCSY
11122D 1H-15N HSQC
11222D 1H-13C HSQC aliphatic
11313D 1H-15N NOESY
11414D CC-NOESY
11513D (H)CCH-TOCSY
11612D 1H-15N HSQC-Histidine
11712D 1H-15N HSQC NH2 only
11813D HBHA(CO)NH
11913D (H)CCH-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.76 mM [U-100% 13C; U-100% 15N] CgR160.003, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.83 mM [U-5% 13C; U-100% 15N] CgR160.0035, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.76 mMCgR160.003-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
5 mMCaCL2-41
100 mMNaCL-51
1 %Proteinase Inhibitors-61
20 mMMES pH 6.5-71
10 %D2O-81
50 uMDSS-91
0.83 mMCgR160.0035-10[U-5% 13C; U-100% 15N]2
0.02 %NaN3-112
10 mMDTT-122
5 mMCaCL2-132
100 mMNaCL-142
1 %Proteinase Inhibitors-152
20 mMMES pH 6.5-162
10 %D2O-172
50 uMDSS-182
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Varian INOVAVarianINOVA6002

-
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
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / 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://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