[English] 日本語
Yorodumi
- PDB-2kcu: NMR solution structure of an uncharacterized protein from Chlorob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kcu
TitleNMR solution structure of an uncharacterized protein from Chlorobium tepidum. Northeast Structural Genomics target CtR107
Componentsprotein CtR107
Keywordsstructural genomics / unknown function / Protein structure / PSI / NESGC / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Bacterial transcription activator effector binding domain-containing protein
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsMills, J.L. / Zhang, Q. / Sukumaran, D.K. / Wang, D. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. ...Mills, J.L. / Zhang, Q. / Sukumaran, D.K. / Wang, D. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of an uncharacterized protein from Chlorobium tepidum. Northeast Structural Genomics target CtR107
Authors: Mills, J.L. / Zhang, Q. / Sukumaran, D.K. / Wang, D. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G. / Szyperski, T.
History
DepositionDec 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references / Structure summary
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: protein CtR107


Theoretical massNumber of molelcules
Total (without water)18,1361
Polymers18,1361
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 protein CtR107


Mass: 18136.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: CT0179 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KFZ1
Sequence detailsALA AT POSITION 27 IS NOT A MUTATION COMPARED TO THE SEQUENCE REFERENCE, BUT A NATURALLY OCCURRING ...ALA AT POSITION 27 IS NOT A MUTATION COMPARED TO THE SEQUENCE REFERENCE, BUT A NATURALLY OCCURRING VARIATION BETWEEN STRAINS OF THE SAME ORGANISM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D (H)CCH-COSY
1813D simultaneous NCaliCaro HH NOESY
1922D 1H-13C HSQC
11022D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.45 mM [U-99% 13C; U-99% 15N] CtR107-1, 5 % [U-2H] D2O-2, 95 % H2O-3, 50 uM DSS-4, 10 mM DTT-5, 0.02 % sodium azide-6, 5 mM calcium chloride-7, 100 mM sodium chloride-8, 20 mM MES-9, 90% H2O/10% D2O90% H2O/10% D2O
20.45 mM [U-5% 13C; U-99% 15N] CtR107-10, 5 % [U-2H] D2O-11, 95 % H2O-12, 50 uM DSS-13, 10 mM DTT-14, 0.02 % sodium azide-15, 5 mM calcium chloride-16, 100 mM sodium chloride-17, 20 mM MES-18, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.45 mMCtR107-1[U-99% 13C; U-99% 15N]1
5 %D2O-2[U-2H]1
95 %H2O-31
50 uMDSS-41
10 mMDTT-51
0.02 %sodium azide-61
5 mMcalcium chloride-71
100 mMsodium chloride-81
20 mMMES-91
0.45 mMCtR107-10[U-5% 13C; U-99% 15N]2
5 %D2O-11[U-2H]2
95 %H2O-122
50 uMDSS-132
10 mMDTT-142
0.02 %sodium azide-152
5 mMcalcium chloride-162
100 mMsodium chloride-172
20 mMMES-182
Sample conditionsIonic strength: 235 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPSCANGlaserprocessing
XEASYBartels et al.chemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CSI(CSI) Wishart and Sykesstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PSVSBhattacharya and Montelionerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / 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