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- PDB-7q3t: Crystal structure of the OmpK36 D insertion chimera from Klebsiel... -

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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 / cell outer membrane / monoatomic ion transmembrane transport / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 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)

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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

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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 %

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