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- PDB-6rck: Crystal structure of the OmpK36 GD insertion chimera from Klebsie... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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