[English] 日本語
Yorodumi
- PDB-2kc7: Solution NMR structure of Bacteroides fragilis protein BF1650. No... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kc7
TitleSolution NMR structure of Bacteroides fragilis protein BF1650. Northeast Structural Genomics Consortium target BfR218
Componentsbfr218_protein
Keywordsstructural genomics / unknown function / tetratricopeptide repeat / all-alpha / GFT-NMR / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...: / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
TPR_REGION domain-containing protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Wu, Y. / Sukumaran, D. / Lee, H. / Lee, D.Y. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. ...Eletsky, A. / Wu, Y. / Sukumaran, D. / Lee, H. / Lee, D.Y. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of Bacteroides fragilis protein BF1650. Northeast Structural Genomics Consortium target BfR218
Authors: Eletsky, A. / Wu, Y. / Sukumaran, D. / Lee, H. / Lee, D.Y. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / ...Authors: Eletsky, A. / Wu, Y. / Sukumaran, D. / Lee, H. / Lee, D.Y. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H. / Szyperski, T.
History
DepositionDec 17, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: bfr218_protein


Theoretical massNumber of molelcules
Total (without water)11,6581
Polymers11,6581
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein bfr218_protein


Mass: 11658.081 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: BF1650 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q64VS8

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC ali
1312D 1H-13C HSQC aro
1412D 1H-13C CT-HSQC ali
1512D 1H-13C CT-HSQC aro
1613D HNNCO
171(4,3)D GFT CABCA(CO)NHN
181(4,3)D GFT HNNCABCA
191(4,3)D HABCAB(CO)NHN
1101(4,3)D GFT (H)CCH-COSY ali
1111(4,3)D GFT (H)CCH-COSY aro
11213D (H)CCH-TOCSY ali
11313D HN(CA)CO
11413D 1H-15N,13C NOESY
11522D 1H-13C CT-HSQC ali 28ms
11612D MEXICO
11732D 1H-15N HSQC
11832D 1H-15N TROSY
11922D 1H-15N HSQC
12022D 1H-15N TROSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
120 mM MES-1, 200 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 50 uM DSS-5, 0.02 % sodium azide-6, 1 X protease inhibitiors-7, 0.89 mM [U-100% 13C; U-100% 15N] bfr218 protein-8, 90% H2O/10% D2O90% H2O/10% D2O
220 mM MES-9, 200 mM sodium chloride-10, 5 mM calcium chloride-11, 10 mM DTT-12, 50 uM DSS-13, 0.02 % sodium azide-14, 1 X protease inhibitiors-15, 1 mM [U-5% 13C; U-100% 15N] bfr218 protein-16, 90% H2O/10% D2O90% H2O/10% D2O
320 mM MES-17, 200 mM sodium chloride-18, 5 mM calcium chloride-19, 10 mM DTT-20, 50 uM DSS-21, 0.02 % sodium azide-22, 1 X protease inhibitiors-23, 1 mM [U-5% 13C; U-100% 15N] bfr218 protein-24, 2.65 G/L PF1 PHAGE-25, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingSolution-ID
20 mMMES-11
200 mMsodium chloride-21
5 mMcalcium chloride-31
10 mMDTT-41
50 uMDSS-51
0.02 %sodium azide-61
%protease inhibitiors-71
0.89 mMbfr218 protein-8[U-100% 13C; U-100% 15N]1
20 mMMES-92
200 mMsodium chloride-102
5 mMcalcium chloride-112
10 mMDTT-122
50 uMDSS-132
0.02 %sodium azide-142
%protease inhibitiors-152
1 mMbfr218 protein-16[U-5% 13C; U-100% 15N]2
20 mMMES-173
200 mMsodium chloride-183
5 mMcalcium chloride-193
10 mMDTT-203
50 uMDSS-213
0.02 %sodium azide-223
%protease inhibitiors-233
1 mMbfr218 protein-24[U-5% 13C; U-100% 15N]3
25 %phage-253
Sample conditionsIonic strength: 215 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA5004

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.0.2Guntertprocessing
CARA1.8.4.2Keller and Wuthrichdata analysis
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
CARA1.8.4.2Keller and Wuthrichpeak picking
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
TALOS2007.068.09.07Cornilescu, Delaglio and Baxdata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: In explicit "water bath"
NMR constraintsNOE constraints total: 2343 / NOE intraresidue total count: 473 / NOE long range total count: 631 / NOE medium range total count: 763 / NOE sequential total count: 567 / Hydrogen bond constraints total count: 200 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.329 Å

+
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