[English] 日本語
Yorodumi
- PDB-2mqc: NMR structure of the protein BVU_0925 from Bacteroides vulgatus A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mqc
TitleNMR structure of the protein BVU_0925 from Bacteroides vulgatus ATCC 8482
ComponentsUncharacterized protein
Keywordsstructural genomics / unknown function / human gut microbiome secreted protein / BACON protein family / PSI-Biology / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


Fimbrillin-like 1, N-terminal / Fimbrillin-like 1 / Putative binding domain, N-terminal / Fimbrillin-like / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BACON domain-containing protein
Similarity search - Component
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model13
AuthorsDutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein BVU_0925 from Bacteroides vulgatus ATCC 8482
Authors: Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K.
History
DepositionJun 18, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references / Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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)11,2961
Polymers11,2961
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)20 / 80target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Uncharacterized protein


Mass: 11296.254 Da / Num. of mol.: 1 / Fragment: UNP residues 425-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Strain: ATCC 8482 / Gene: BVU_0925 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: A6KYV6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111APSY 4D-HACANH
121APSY 5D-(HA)CA(CO)NH
131APSY 5D-CBCA(CO)NH
1412D 1H-15N HSQC
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 1.2 mM [U-99% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-99% 13C; U-98% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
5 mMsodium azide-41
Sample conditionsIonic strength: 0.0798 / pH: 6.0 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert P.refinement
CYANAGuntert P.geometry optimization
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
OPALLuginbuhl, Guntert, Billeter and Wuthrichgeometry optimization
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
j-UNIOHerrmann, Guntert and Wuthrichpeak picking
j-UNIOHerrmann, Guntert and Wuthrichchemical shift assignment
j-UNIOHerrmann, Guntert and Wuthrichstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1375 / NOE intraresidue total count: 343 / NOE long range total count: 505 / NOE medium range total count: 115 / NOE sequential total count: 412
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / 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