[English] 日本語
Yorodumi
- PDB-5n9h: STRUCTURE OF 283-LGNY-286, THE STERIC ZIPPER THAT SUPPORTS THE SE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n9h
TitleSTRUCTURE OF 283-LGNY-286, THE STERIC ZIPPER THAT SUPPORTS THE SELF-ASSOCIATION OF P. STUARTII OMP-PST2 INTO DIMERS OF TRIMERS
ComponentsPorin
KeywordsCELL ADHESION / STERIC-ZIPPER / PORIN / MICRO-CRYSTAL / SELF-ASSOCIATION
Function / homology:
Function and homology information
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.997 Å
AuthorsNasrallah, C. / Colletier, J.P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE18-0005-02 France
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Porin self-association enables cell-to-cell contact in
Authors: El-Khatib, M. / Nasrallah, C. / Lopes, J. / Tran, Q.T. / Tetreau, G. / Basbous, H. / Fenel, D. / Gallet, B. / Lethier, M. / Bolla, J.M. / Pages, J.M. / Vivaudou, M. / Weik, M. / ...Authors: El-Khatib, M. / Nasrallah, C. / Lopes, J. / Tran, Q.T. / Tetreau, G. / Basbous, H. / Fenel, D. / Gallet, B. / Lethier, M. / Bolla, J.M. / Pages, J.M. / Vivaudou, M. / Weik, M. / Winterhalter, M. / Colletier, J.P.
History
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Porin
B: Porin
C: Porin
M: Porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0546
Polymers1,8624
Non-polymers1922
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-15 kcal/mol
Surface area2700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)4.784, 11.546, 47.044
Angle α, β, γ (deg.)90.01, 90.01, 90.01
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide
Porin


Mass: 465.501 Da / Num. of mol.: 4 / Fragment: DIMERIZATION DOMAIN, UNP residues 305-308 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria) / References: UniProt: A0A0L6X8Y0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.45 Å3/Da / Density % sol: 15.4 % / Description: Needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 3.2 M AMMONIUM SULFATE; 0.1 M BUFFER ACID CITRIC PH4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 0.997→47.04 Å / Num. obs: 4934 / % possible obs: 89.7 % / Observed criterion σ(I): 5.5 / Redundancy: 2.17 % / Biso Wilson estimate: 1.68 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.81
Reflection shellResolution: 1→1.06 Å / Redundancy: 2.12 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.47 / % possible all: 87.4

-
Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHELXEphasing
PHENIXrefinement
SHELXLphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.997→23.522 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 2.03 / Phase error: 8.97
RfactorNum. reflection% reflection
Rfree0.0959 246 5 %
Rwork0.0811 --
obs0.0818 4918 89.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 2.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.1048 Å20.3781 Å2-0.0048 Å2
2---0.422 Å20.3629 Å2
3----0.2565 Å2
Refinement stepCycle: LAST / Resolution: 0.997→23.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms132 0 10 8 150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013148
X-RAY DIFFRACTIONf_angle_d1.929200
X-RAY DIFFRACTIONf_dihedral_angle_d11.33844
X-RAY DIFFRACTIONf_chiral_restr0.11316
X-RAY DIFFRACTIONf_plane_restr0.00724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9972-1.25640.11671210.09712306X-RAY DIFFRACTION87
1.2564-23.52850.08311250.07162366X-RAY DIFFRACTION91

+
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