[English] 日本語
Yorodumi
- PDB-6rck: Crystal structure of the OmpK36 GD insertion chimera from Klebsie... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rck
TitleCrystal structure of the OmpK36 GD insertion chimera from Klebsiella pneumonia
ComponentsOmpK36
KeywordsMEMBRANE PROTEIN / OmpK36 GD chimera
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / 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: 2.029 Å
AuthorsBeis, K. / Romano, M. / Kwong, J.
CitationJournal: Nat Commun / Year: 2019
Title: OmpK36-mediated Carbapenem resistance attenuates ST258 Klebsiella pneumoniae in vivo.
Authors: Wong, J.L.C. / Romano, M. / Kerry, L.E. / Kwong, H.S. / Low, W.W. / Brett, S.J. / Clements, A. / Beis, K. / Frankel, G.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: OmpK36
B: OmpK36
C: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,58015
Polymers114,6933
Non-polymers3,88712
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Homology to other porins including entry 5O79
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-35 kcal/mol
Surface area39520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.458, 74.412, 90.112
Angle α, β, γ (deg.)90.00, 111.73, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein OmpK36 / OmpK36 porin / Outer membrane protein C


Mass: 38231.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Contains insertion of G113D114 in the mature protein
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompK36, ompC_2, DDJ63_09115, NCTC13443_05288 / Production host: Escherichia coli (E. coli) / Variant (production host): Omp8 / References: UniProt: D6QLY1
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical ChemComp-P6L / (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P / Comment: phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.029→57.37 Å / Num. obs: 92398 / % possible obs: 99.8 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.1
Reflection shellResolution: 2.029→2.06 Å / Rmerge(I) obs: 0.811 / Num. unique obs: 4538 / CC1/2: 0.58

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o79

5o79


Resolution: 2.029→55.729 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.85
RfactorNum. reflection% reflection
Rfree0.2461 4669 5.06 %
Rwork0.2078 --
obs0.2097 92323 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.029→55.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8091 0 147 342 8580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078403
X-RAY DIFFRACTIONf_angle_d0.85911335
X-RAY DIFFRACTIONf_dihedral_angle_d7.9754783
X-RAY DIFFRACTIONf_chiral_restr0.0521132
X-RAY DIFFRACTIONf_plane_restr0.0041512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0291-2.05210.32581570.27012868X-RAY DIFFRACTION97
2.0521-2.07630.29321550.25562868X-RAY DIFFRACTION100
2.0763-2.10160.2981480.25552903X-RAY DIFFRACTION100
2.1016-2.12820.27311630.25322926X-RAY DIFFRACTION100
2.1282-2.15620.29631400.24012882X-RAY DIFFRACTION100
2.1562-2.18570.28141830.23582883X-RAY DIFFRACTION100
2.1857-2.2170.31281530.23262910X-RAY DIFFRACTION100
2.217-2.250.27011750.23032947X-RAY DIFFRACTION100
2.25-2.28520.26291660.23082845X-RAY DIFFRACTION100
2.2852-2.32270.27781510.22472947X-RAY DIFFRACTION100
2.3227-2.36270.27651610.23032873X-RAY DIFFRACTION100
2.3627-2.40570.28891640.22222925X-RAY DIFFRACTION100
2.4057-2.4520.27881730.23092876X-RAY DIFFRACTION100
2.452-2.5020.29621540.22122936X-RAY DIFFRACTION100
2.502-2.55640.27111500.21552918X-RAY DIFFRACTION100
2.5564-2.61590.25131370.21422901X-RAY DIFFRACTION100
2.6159-2.68130.25311440.20642951X-RAY DIFFRACTION100
2.6813-2.75380.26141830.21232899X-RAY DIFFRACTION100
2.7538-2.83480.24461750.2062904X-RAY DIFFRACTION100
2.8348-2.92630.23431410.19382930X-RAY DIFFRACTION100
2.9263-3.03090.241720.2042869X-RAY DIFFRACTION100
3.0309-3.15220.23031330.19612954X-RAY DIFFRACTION100
3.1522-3.29570.22271660.19182925X-RAY DIFFRACTION99
3.2957-3.46940.26421270.19342958X-RAY DIFFRACTION100
3.4694-3.68680.25091560.22945X-RAY DIFFRACTION100
3.6868-3.97130.24431930.20622903X-RAY DIFFRACTION100
3.9713-4.37080.21571470.18752982X-RAY DIFFRACTION100
4.3708-5.0030.18611640.17192952X-RAY DIFFRACTION100
5.003-6.30180.21731150.19672991X-RAY DIFFRACTION100
6.3018-55.75040.21611230.22233083X-RAY DIFFRACTION99

+
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