[English] 日本語
Yorodumi
- PDB-7q3t: Crystal structure of the OmpK36 D insertion chimera from Klebsiel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q3t
TitleCrystal structure of the OmpK36 D insertion chimera from Klebsiella pneumonia
ComponentsOmpK36
KeywordsMEMBRANE PROTEIN / outer membrane porin
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / metal ion binding
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 domain superfamily
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.788 Å
AuthorsKwong, H. / Beis, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N020103/1 United Kingdom
CitationJournal: Plos Pathog. / Year: 2022
Title: Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae.
Authors: David, S. / Wong, J.L.C. / Sanchez-Garrido, J. / Kwong, H.S. / Low, W.W. / Morecchiato, F. / Giani, T. / Rossolini, G.M. / Brett, S.J. / Clements, A. / Beis, K. / Aanensen, D.M. / Frankel, G.
History
DepositionOct 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OmpK36
B: OmpK36
C: OmpK36
D: OmpK36
E: OmpK36
F: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,53065
Polymers229,0446
Non-polymers14,48659
Water16,952941
1
A: OmpK36
B: OmpK36
C: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,14437
Polymers114,5223
Non-polymers8,62234
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18020 Å2
ΔGint-39 kcal/mol
Surface area42360 Å2
MethodPISA
2
D: OmpK36
E: OmpK36
F: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,38628
Polymers114,5223
Non-polymers5,86425
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-23 kcal/mol
Surface area42920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.024, 73.606, 158.663
Angle α, β, γ (deg.)91.04, 97.26, 103.16
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
OmpK36


Mass: 38174.012 Da / Num. of mol.: 6 / Mutation: D115 insertion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompK36 / Production host: Escherichia coli (E. coli) / References: UniProt: D6QLY0
#2: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical
ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 941 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Lithium sulfate, 0.1 M Sodium citrate, and 10% PEG 4000 (pH 5.6)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.78→78.6 Å / Num. obs: 221416 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.84 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.154 / Net I/σ(I): 6
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 1.296 / Mean I/σ(I) obs: 1 / Num. unique obs: 10907 / CC1/2: 0.34 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
autoPROCdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rd3

6rd3


Resolution: 1.788→78.6 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 11110 5.02 %RANDOM
Rwork0.1855 ---
obs0.1869 221336 97.4 %-
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.0677 Å2-0.2414 Å2-0.2579 Å2
2--0.4039 Å2-0.4794 Å2
3----3.4717 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.788→78.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16218 0 605 941 17764
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00817133HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9822970HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5997SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3009HARMONIC5
X-RAY DIFFRACTIONt_it17133HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion17.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1999SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15077SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.8 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2395 227 5.13 %
Rwork0.2308 4200 -
all0.2312 4427 -
obs--95.66 %

+
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://pdbjlvh1.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