[English] 日本語
Yorodumi
- PDB-5ird: Solution structure of Rv1466 from Mycobacterium tuberculosis, a p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ird
TitleSolution structure of Rv1466 from Mycobacterium tuberculosis, a protein associated with [Fe-S] complex assembly and repair - Seattle Structural Genomics Center for Infectious Disease target MytuD.17486.a
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / infectious disease / TB / [Fe-S] complexes / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyMIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily / FeS_assembly_P domain-containing protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200025C United States
CitationJournal: To Be Published
Title: Solution structure of Rv1466, a Mycobacterium tuberculosis protein associated with [Fe-S] cluster assembly and repair.
Authors: Buchko, G.W. / Hewitt, S.N. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
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


Theoretical massNumber of molelcules
Total (without water)12,6881
Polymers12,6881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Uncharacterized protein / Rv1466


Mass: 12688.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: MRA_1475 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A5U2G9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic32D 1H-15N HSQC
121anisotropic42D 1H-13C HSQC aliphatic
131anisotropic42D 1H-13C HSQC aromatic
141anisotropic23D HN(CA)CB
151anisotropic33D CBCA(CO)NH
171anisotropic33D HNCO
161anisotropic33D H(CCO)NH
1101anisotropic13D C(CO)NH
191anisotropic32D Delta
182anisotropic3Deuterium exchange
1121anisotropic33D 1H-15N NOESY
1111anisotropic43D 1H-13C NOESY aliphatic
1131anisotropic33D 1H-13C NOESY aromatic

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-13C; U-15N] Rv1466, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2ORv146693% H2O/7% D2O
solution20.5 mM [U-15N] Rv1466, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2ORv14666_N15100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRv1466[U-13C; U-15N]1
100 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance1
1 mMDTTnatural abundance1
0.5 mMRv1466[U-15N]2
100 mMsodium chloridenatural abundance2
20 mMTRISnatural abundance2
1 mMDTTnatural abundance2
Sample conditionsIonic strength: .12 M / Ionic strength err: 0.005 / Label: Condition_1 / pH: 7 / PH err: 0.2 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.5

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian VXRSVarianVXRS7503
Varian VXRSVarianVXRS8004

-
Processing

NMR software
NameVersionDeveloperClassification
Sparky3.115Goddarddata analysis
Sparky3.115Goddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Felix2007Accelrys Software Inc.processing
PSVS1.5Bhattacharya and Montelionedata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 2
Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 5.0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS.
NMR representativeSelection criteria: closest to the average
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://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