[English] 日本語
Yorodumi
- PDB-6cah: NMR-based structure of the FHA-2 domain from Mycobacterium tuberc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cah
TitleNMR-based structure of the FHA-2 domain from Mycobacterium tuberculosis ABC transporter Rv1747
ComponentsABC transporter ATP-binding/permease protein Rv1747
KeywordsPROTEIN BINDING / permuted Forkhead-associated domain / beta-sandwich / phosphothreonine binding / ABC transporter
Function / homology
Function and homology information


Translocases / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / peptidoglycan-based cell wall / transmembrane transport / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
ABC-2 type transporter / ABC-2 type transporter / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC-2 type transporter / ABC-2 type transporter / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter ATP-binding/permease protein Rv1747
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHeinkel, F. / Okon, M. / Gsponer, J. / McIntosh, L.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2018
Title: Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747.
Authors: Heinkel, F. / Shen, L. / Richard-Greenblatt, M. / Okon, M. / Bui, J.M. / Gee, C.L. / Gay, L.M. / Alber, T. / Av-Gay, Y. / Gsponer, J. / McIntosh, L.P.
History
DepositionJan 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter ATP-binding/permease protein Rv1747


Theoretical massNumber of molelcules
Total (without water)11,6021
Polymers11,6021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8720 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

#1: Protein ABC transporter ATP-binding/permease protein Rv1747


Mass: 11602.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv1747 / Production host: Escherichia coli (E. coli)
References: UniProt: O65934, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
1121isotropic12D 1H-13C HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D (H)CCH-TOCSY
1111isotropic13D H(CCO)NH
1101isotropic13D CC(CO)NH
191isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-13C NOESY aromatic

-
Sample preparation

DetailsType: solution
Contents: 300 uM [U-100% 13C; U-100% 15N] Rv1747 FHA-2, 20 mM Sodium Phosphate, 100 mM NaCl, water
Label: 15N/13C FHA-2 NMR sample / Solvent system: water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMRv1747 FHA-2[U-100% 13C; U-100% 15N]1
20 mMSodium Phosphate1
100 mMNaCl1
Sample conditionsIonic strength: 100 mM / Label: standard FHA NMR conditions / pH: 6 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMReRyu, Lim, Sung and Leerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / 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