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- PDB-6v78: OmpK37 porin -

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Basic information

Entry
Database: PDB / ID: 6v78
TitleOmpK37 porin
ComponentsOmpK37
KeywordsMEMBRANE PROTEIN / Porin Gram-negative outer membrane protein
Function / homology
Function and homology information


porin activity / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin domain, Gram-negative type / 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: 2.6 Å
AuthorsRocker, A. / Lithgow, T.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)1092262 Australia
CitationJournal: Mbio / Year: 2020
Title: Global Trends in Proteome Remodeling of the Outer Membrane Modulate Antimicrobial Permeability in Klebsiella pneumoniae.
Authors: Rocker, A. / Lacey, J.A. / Belousoff, M.J. / Wilksch, J.J. / Strugnell, R.A. / Davies, M.R. / Lithgow, T.
History
DepositionDec 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: OmpK37
B: OmpK37
C: OmpK37


Theoretical massNumber of molelcules
Total (without water)119,5263
Polymers119,5263
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-54 kcal/mol
Surface area43030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.520, 138.510, 91.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein OmpK37 / Outer membrane pore protein N / non-specific / Outer membrane protein N / Porin OmpK37 / Porin OmpN ...Outer membrane pore protein N / non-specific / Outer membrane protein N / Porin OmpK37 / Porin OmpN / Porin OmpS2


Mass: 39842.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: ompK37, ompN_1, ompN_2, ompS2, BANRA_00477, C3483_14590, C3F39_02150, C7V41_10070, CSC88_04530, DD581_25170, FJR44_14030, FNY87_08485, NCTC11679_03052, NCTC13465_01341, NCTC13635_00771, PMK1_ ...Gene: ompK37, ompN_1, ompN_2, ompS2, BANRA_00477, C3483_14590, C3F39_02150, C7V41_10070, CSC88_04530, DD581_25170, FJR44_14030, FNY87_08485, NCTC11679_03052, NCTC13465_01341, NCTC13635_00771, PMK1_03772, SAMEA104305404_06668, SAMEA104567806_00300, SAMEA23986918_02116
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S5UCA2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.125M SPG buffer (succinic acid, sodium dihydrogen phosphate, glycine), 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 43308 / % possible obs: 99.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 45.56 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.193 / Net I/σ(I): 11.11
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 4766 / CC1/2: 0.692 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OSM

1osm


Resolution: 2.6→49.34 Å / SU ML: 0.4427 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.3877
RfactorNum. reflection% reflection
Rfree0.3228 2167 5 %
Rwork0.2569 --
obs0.2602 43298 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8382 0 0 73 8455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00858565
X-RAY DIFFRACTIONf_angle_d1.082411586
X-RAY DIFFRACTIONf_chiral_restr0.05961158
X-RAY DIFFRACTIONf_plane_restr0.00681563
X-RAY DIFFRACTIONf_dihedral_angle_d20.04493030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.39551410.34722670X-RAY DIFFRACTION98.63
2.66-2.730.41141420.33952705X-RAY DIFFRACTION98.96
2.73-2.80.41021420.32462702X-RAY DIFFRACTION98.96
2.8-2.880.42391410.32642689X-RAY DIFFRACTION98.81
2.88-2.980.37481420.29912700X-RAY DIFFRACTION99.23
2.98-3.080.35531430.28642707X-RAY DIFFRACTION99.16
3.08-3.210.32121430.26892725X-RAY DIFFRACTION99.27
3.21-3.350.36651420.27652693X-RAY DIFFRACTION99.02
3.35-3.530.37151460.27992757X-RAY DIFFRACTION99.52
3.53-3.750.3891440.26472734X-RAY DIFFRACTION99.45
3.75-4.040.31411440.24742737X-RAY DIFFRACTION99.45
4.04-4.450.26941450.20952761X-RAY DIFFRACTION99.62
4.45-5.090.23211480.19962805X-RAY DIFFRACTION99.83
5.09-6.410.26481480.2222814X-RAY DIFFRACTION99.97
6.41-49.340.31671560.2612932X-RAY DIFFRACTION99.17

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