[English] 日本語
Yorodumi
- PDB-6v78: OmpK37 porin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v78
TitleOmpK37 porin
ComponentsOmpK37
KeywordsMEMBRANE PROTEIN / Porin Gram-negative outer membrane protein
Function / homology
Function and homology information


porin activity / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRocker, A. / Lithgow, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)1092262 Australia
CitationJournal: Mbio / Year: 2020
Title: Global Trends in Proteome Remodeling of the Outer Membrane Modulate Antimicrobial Permeability in Klebsiella pneumoniae.
Authors: Rocker, A. / Lacey, J.A. / Belousoff, M.J. / Wilksch, J.J. / Strugnell, R.A. / Davies, M.R. / Lithgow, T.
History
DepositionDec 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OmpK37
B: OmpK37
C: OmpK37


Theoretical massNumber of molelcules
Total (without water)119,5263
Polymers119,5263
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-54 kcal/mol
Surface area43030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.520, 138.510, 91.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein OmpK37 / Outer membrane pore protein N / non-specific / Outer membrane protein N / Porin OmpK37 / Porin OmpN ...Outer membrane pore protein N / non-specific / Outer membrane protein N / Porin OmpK37 / Porin OmpN / Porin OmpS2


Mass: 39842.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: ompK37, ompN_1, ompN_2, ompS2, BANRA_00477, C3483_14590, C3F39_02150, C7V41_10070, CSC88_04530, DD581_25170, FJR44_14030, FNY87_08485, NCTC11679_03052, NCTC13465_01341, NCTC13635_00771, PMK1_ ...Gene: ompK37, ompN_1, ompN_2, ompS2, BANRA_00477, C3483_14590, C3F39_02150, C7V41_10070, CSC88_04530, DD581_25170, FJR44_14030, FNY87_08485, NCTC11679_03052, NCTC13465_01341, NCTC13635_00771, PMK1_03772, SAMEA104305404_06668, SAMEA104567806_00300, SAMEA23986918_02116
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S5UCA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.125M SPG buffer (succinic acid, sodium dihydrogen phosphate, glycine), 20% PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 43308 / % possible obs: 99.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 45.56 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.193 / Net I/σ(I): 11.11
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 4766 / CC1/2: 0.692 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OSM

1osm


Resolution: 2.6→49.34 Å / SU ML: 0.4427 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.3877
RfactorNum. reflection% reflection
Rfree0.3228 2167 5 %
Rwork0.2569 --
obs0.2602 43298 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8382 0 0 73 8455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00858565
X-RAY DIFFRACTIONf_angle_d1.082411586
X-RAY DIFFRACTIONf_chiral_restr0.05961158
X-RAY DIFFRACTIONf_plane_restr0.00681563
X-RAY DIFFRACTIONf_dihedral_angle_d20.04493030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.39551410.34722670X-RAY DIFFRACTION98.63
2.66-2.730.41141420.33952705X-RAY DIFFRACTION98.96
2.73-2.80.41021420.32462702X-RAY DIFFRACTION98.96
2.8-2.880.42391410.32642689X-RAY DIFFRACTION98.81
2.88-2.980.37481420.29912700X-RAY DIFFRACTION99.23
2.98-3.080.35531430.28642707X-RAY DIFFRACTION99.16
3.08-3.210.32121430.26892725X-RAY DIFFRACTION99.27
3.21-3.350.36651420.27652693X-RAY DIFFRACTION99.02
3.35-3.530.37151460.27992757X-RAY DIFFRACTION99.52
3.53-3.750.3891440.26472734X-RAY DIFFRACTION99.45
3.75-4.040.31411440.24742737X-RAY DIFFRACTION99.45
4.04-4.450.26941450.20952761X-RAY DIFFRACTION99.62
4.45-5.090.23211480.19962805X-RAY DIFFRACTION99.83
5.09-6.410.26481480.2222814X-RAY DIFFRACTION99.97
6.41-49.340.31671560.2612932X-RAY DIFFRACTION99.17

+
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