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- PDB-7pzf: Crystal structure of the OmpK36 TD insertion chimera from Klebsie... -

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Basic information

Entry
Database: PDB / ID: 7pzf
TitleCrystal structure of the OmpK36 TD 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
TETRADECANE / : / OmpK36
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 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 12, 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

Downloads & links

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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)233,87936
Polymers229,6516
Non-polymers4,22930
Water21,7261206
1
A: OmpK36
B: OmpK36
C: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,02817
Polymers114,8253
Non-polymers2,20314
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-115 kcal/mol
Surface area39420 Å2
MethodPISA
2
D: OmpK36
E: OmpK36
F: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,85119
Polymers114,8253
Non-polymers2,02616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-127 kcal/mol
Surface area39800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.106, 73.428, 158.837
Angle α, β, γ (deg.)91.12, 97.17, 103.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
OmpK36


Mass: 38275.113 Da / Num. of mol.: 6 / Mutation: T115 and D116 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-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Li
#3: Chemical...
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C14H30
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1206 / 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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.499→54.25 Å / Num. obs: 369351 / % possible obs: 95.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.54 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1 / Num. unique obs: 17954 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RD3

6rd3


Resolution: 1.499→54.25 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.069
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 18383 4.98 %RANDOM
Rwork0.1901 ---
obs0.1909 369148 95.7 %-
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.7842 Å2-3.8572 Å2-0.913 Å2
2--4.4023 Å20.4878 Å2
3----5.1866 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.499→54.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16226 0 249 1206 17681
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00816952HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9922912HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5810SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3060HARMONIC5
X-RAY DIFFRACTIONt_it16733HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.26
X-RAY DIFFRACTIONt_other_torsion15.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2033SEMIHARMONIC5
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_contact15704SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.51 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2462 360 4.88 %
Rwork0.2214 7023 -
all0.2227 7383 -
obs--88.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0592-0.0934-0.03320.1964-0.02260.1634-0.0063-0.006-0.0422-0.01240.003-0.00180.0172-0.0140.0033-0.0234-0.0654-0.00730.0310.0011-0.04578.6496-22.37913.8937
2-0.0097-0.0290.00590.3266-0.03340.3195-0.02470.0165-0.0024-0.01780.0130.0057-0.0257-0.00670.0118-0.0319-0.061-0.01010.03960.0072-0.06123.142810.7648-14.691
3-0.0017-0.05040.00880.3321-0.03760.3766-0.0061-0.02320.01840.05770.01290.0037-0.0544-0.0238-0.0069-0.013-0.0558-0.00140.02940.008-0.0657-1.1139.104123.4624
4-0.00620.0118-0.07220.39530.02620.2319-0.00560.0183-0.0372-0.0017-0.006-0.02240.02010.01110.0116-0.0366-0.0502-0.00550.03140.0095-0.0477-16.4363-31.580280.3437
50.0714-0.1374-0.03910.2579-0.060.2458-0.0279-0.05020.01830.0520.0059-0.0153-0.02990.00730.0221-0.0188-0.0612-0.01210.03730.0043-0.0595-26.36520.396998.9174
60.0018-0.0527-0.01950.34930.04070.3505-0.01270.00960.0088-0.0522-0.0046-0.02510.00760.01820.0172-0.0363-0.0564-0.00070.04410.0127-0.0623-20.69541.459861.084
70.13950.0284-0.00840.1462-0.0205-0.0071-0.02250.0144-0.0281-0.0228-0.0023-0.0010.0088-0.0320.02470.2283-0.0162-0.03930.2099-0.00610.1891-9.413-2.713644.8461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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