[English] 日本語
Yorodumi
- PDB-2m4e: Solution NMR structure of VV2_0175 from Vibrio vulnificus, NESG t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m4e
TitleSolution NMR structure of VV2_0175 from Vibrio vulnificus, NESG target VnR1 and CSGID target IDP91333
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / pathogenic bacterial protein / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyUncharacterised protein PF16691 family / Protein of unknown function DUF5062 / DUF5062 superfamily / Domain of unknown function (DUF5062) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / DUF5062 domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsWu, B. / Yee, A. / Houliston, S. / Lemak, A. / Garcia, M. / Savchenko, A. / Arrowsmith, C.H. / Anderson, W.F. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP) / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Solution NMR structure of VV2_0175 from Vibrio vulnificus, NESG target VnR1 and CSGID target IDP91333
Authors: Wu, B. / Yee, A. / Houliston, S. / Lemak, A. / Garcia, M. / Savchenko, A. / Arrowsmith, C.H.
History
DepositionFeb 4, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Feb 8, 2017Group: Structure summary
Revision 1.3Jun 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 1.4May 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: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,2741
Polymers12,2741
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Putative uncharacterized protein


Mass: 12274.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV2_0175 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8D7H8, UniProt: A0A3Q0KXE9*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY aromatic
11022D 1H-13C HSQC
11113D HN(CA)CB
11213D HNCB
11313D C(CO)NH
11413D H(CCO)NH
11513D (H)CCH-COSY
11613D TOCSY-HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] VV2_0175, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 % inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
20.2 mM [U-7% 13C; U-100% 15N] VV2_0175, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 % inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMVV2_0175-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 mMDTT-4[U-100% 2H]1
0.01 %NaN3-51
10 mMbenzamidine-61
1 %inhibitor cocktail-71
0.2 mMVV2_0175-8[U-7% 13C; U-100% 15N]2
10 mMTRIS-9[U-100% 2H]2
300 mMsodium chloride-102
10 mMDTT-11[U-100% 2H]2
0.01 %NaN3-122
10 mMbenzamidine-132
1 %inhibitor cocktail-142
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas, Arrowsmithprocessing
Sparky3.95Goddarddata analysis
FMCGUI2.4Lemak, Arrowsmithchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
FAWNLemak, Arrowsmithchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The heterogeneity of viv0002 expressed in Escherichia coli BL21 (DE3) was observed. Three extra peaks in 15N HSQC and more than 25 extra peaks in 13C HSQC were identified. These peaks are ...Details: The heterogeneity of viv0002 expressed in Escherichia coli BL21 (DE3) was observed. Three extra peaks in 15N HSQC and more than 25 extra peaks in 13C HSQC were identified. These peaks are grouped into three fragments, one assigned as GlcNAc, the other two fragments could not be accurately assigned given the limited information we have, but they are likely to belong to glycans. These fragments display intra NOEs only and remain solvent exposed with strong and narrow line widths. NMR relaxation data showed that these unknown modifications are highly mobile and no interaction with viv0002. Heterologously expressed viv0002 was confirmed by LC-MS. A mass shift of 178 Da of 15N-labeled viv0002 was detected whereas a shift of 72 Da for 13C/15N-labeled sample. However, neither of results matches any three unknown fragments seen in the NMR spectrum with MW 202 Da, 155 Da and 204 Da, respectively. The nature and functional consequence of the unknown fragments/modifications to viv0002 are not understood at this stage. The structure deposited provides the basis of the future investigation.
NMR constraintsNOE constraints total: 2122 / NOE intraresidue total count: 384 / NOE long range total count: 687 / NOE medium range total count: 649 / NOE sequential total count: 402 / Hydrogen bond constraints total count: 70 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 57
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
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