[English] 日本語
Yorodumi
- PDB-1q9f: NMR STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX IN DHPC MICELLES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q9f
TitleNMR STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX IN DHPC MICELLES
ComponentsOuter membrane protein X
KeywordsMEMBRANE PROTEIN / OMPX / TROSY / DHPC / DETERGENTS / LIPIDS / MICELLES
Function / homology
Function and homology information


host outer membrane / membrane => GO:0016020 / cell outer membrane
Similarity search - Function
: / Enterobacterial virulence outer membrane protein signature 1. / Virulence-related outer membrane protein / Enterobacterial virulence outer membrane protein signature 2. / Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Porin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein X / Outer membrane protein X
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS (CANDID)
AuthorsFernandez, C. / Hilty, C. / Wider, G. / Guntert, P. / Wuthrich, K.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: NMR structure of the integral membrane protein OmpX.
Authors: Fernandez, C. / Hilty, C. / Wider, G. / Guntert, P. / Wuthrich, K.
#1: Journal: J.Biomol.NMR / Year: 2002
Title: Side chain NMR assignments in the membrane protein OmpX reconstituted in DHPC micelles
Authors: Hilty, C. / Fernandez, C. / Wider, G. / Wuthrich, K.
#2: Journal: To be Published
Title: Stereospecific assignments of the isopropyl methyl groups of the membrane protein OmpX in DHPC micelles
Authors: Hilty, C. / Wider, G. / Fernandez, C. / Wuthrich, K.
History
DepositionAug 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane protein X


Theoretical massNumber of molelcules
Total (without water)16,3721
Polymers16,3721
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 / 400target function
Representative

-
Components

#1: Protein Outer membrane protein X / OUTER MEMBRANE PROTEIN OMPX


Mass: 16371.768 Da / Num. of mol.: 1 / Mutation: HIS100A to ASN100A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: OMPX / Plasmid: PET3B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P36546, UniProt: P0A917*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
1313D H(C)(CC)-TOCSY-(CO)-[15N,1H]-TROSY
1512D [13C,1H]-HSQC

-
Sample preparation

DetailsContents: 2MM OMPX U-15N,13C,2H; 2MM OMPX U-15N,13C,2H/L,V,ID1- 13CH3; 2MM OMPX U-15N,10%-13C
Sample conditionsIonic strength: 20mM SODIUM PHOSPHATE, 100mM NACL / pH: 6.5 / Pressure: AMBIENT / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX7502
Bruker DRXBrukerDRX5003

-
Processing

NMR software
NameVersionDeveloperClassification
OPALp2.6KORADI, R., LUGINBUHL, P.refinement
CYANA1structure solution
TALOSstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS (CANDID) / Software ordinal: 1
Details: AUTOMATIC IDENTIFICATION OF HYDROGEN BOND CONSTRAINTS
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / 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