[English] 日本語
Yorodumi
- PDB-2lky: Solution structure of MSMEG_1053, the second DUF3349 annotated pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lky
TitleSolution structure of MSMEG_1053, the second DUF3349 annotated protein in the genome of Mycobacterium smegmatis, Seattle Structural Genomics Center for Infectious Disease target MysmA.17112.b
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / infectious disease / tuberculosis / DUF proteins / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homologyDUF3349, helical bundle / DUF3349, helical bundle / Protein of unknown function DUF3349 / Protein of unknown function (DUF3349) / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / EndoIII-related endonuclease
Function and homology information
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Protein Sci. / Year: 2020
Title: Structural diversity in the Mycobacteria DUF3349 superfamily.
Authors: Buchko, G.W. / Abendroth, J. / Robinson, J.I. / Phan, I.Q. / Myler, P.J. / Edwards, T.E.
History
DepositionOct 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2Jun 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 1.3May 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)12,4341
Polymers12,4341
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)17 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Uncharacterized protein


Mass: 12433.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / Gene: MSMEG_1063 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0QRC1
Sequence detailsTHE AUTHORS STATE THAT THE PROTEIN WAS OBTAINED VIA PCR CLONING, AND M5 AND V6 ARE PART OF THE ...THE AUTHORS STATE THAT THE PROTEIN WAS OBTAINED VIA PCR CLONING, AND M5 AND V6 ARE PART OF THE PROTEIN SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-13C NOESY aliphatic
1413D 1H-13C NOESY aromatic
1513D 1H-15N NOESY
1613D HN(CA)CB
1713D HN(COCA)CB
1813D HNCO
1913D C(CO)NH
11012D HBCBCGCDCDHD
11112D (HB)CB(CGCDCE)HE
2122DEUTERIUM EXCHANGE

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 1 mM DTT, 20 mM TRIS, 93% H2O/7% D2O93% H2O/7% D2O
21.0 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 1 mM DTT, 20 mM TRIS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity-1[U-99% 13C; U-99% 15N]1
100 mMsodium chloride-21
1 mMDTT-31
20 mMTRIS-41
1.0 mMentity-5[U-99% 13C; U-99% 15N]2
100 mMsodium chloride-62
1 mMDTT-72
20 mMTRIS-82
Sample conditionsIonic strength: 0.12 / pH: 7 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
Felix2007Accelrys Software Inc.processing
Sparky3.115Goddarddata analysis
Sparky3.115Goddardpeak picking
CNSSOLVE2.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionedata analysis
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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 (CNSSOLVE) AFTER ADDING 1% TO THE UPPER BOUNDARY LIMIT OF THE UPPER DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS. STRUCTURES WITH 3 OR MORE CLOSE CONTACTS FOLLOWING WATER REFINEMENT, AS DETERMINED BY PSVS, WERE REMOVED FROM THE ENSEMBLE. IN THE END, 17 OUT OF THE 20 CYANA STRUCTURES REFINED EXPLICITLY WITH WATER WERE INCLUDED IN THE FINAL DEPOSITION.
NMR constraintsNOE constraints total: 1726 / NOE intraresidue total count: 1272 / NOE long range total count: 344 / NOE medium range total count: 413 / NOE sequential total count: 515 / Protein phi angle constraints total count: 71 / Protein psi angle constraints total count: 71
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 17

+
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