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- PDB-8qxp: Crystal structure of the outer membrane porin OmpW from Klebsiell... -

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Basic information

Entry
Database: PDB / ID: 8qxp
TitleCrystal structure of the outer membrane porin OmpW from Klebsiella pneumoniae
ComponentsOmpW protein
KeywordsMEMBRANE PROTEIN / outer membrane porin
Function / homologyOuter membrane protein, OmpW / OmpW family / outer membrane / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Outer membrane protein OmpW
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSeddon, C. / Beis, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Structure of the outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae.
Authors: Seddon, C. / Frankel, G. / Beis, K.
History
DepositionOct 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OmpW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9703
Polymers20,7781
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-26 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.928, 138.636, 52.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein OmpW protein / Outer membrane protein OmpW


Mass: 20778.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: sequence of mature protein / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompW, BN49_2384, KPZU09_20550 / Production host: Escherichia coli (E. coli) / References: UniProt: W9B759
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.35 M lithium sulphate, 0.1 M sodium acetate pH 4.0, 11% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.2→52.97 Å / Num. obs: 5639 / % possible obs: 99.84 % / Redundancy: 12.7 % / Biso Wilson estimate: 98.04 Å2 / CC1/2: 0.855 / Net I/σ(I): 64
Reflection shellResolution: 3.2→3.315 Å / Num. unique obs: 560 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→52.97 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3117 236 4.19 %RANDOM
Rwork0.2668 ---
obs0.2686 5633 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→52.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 10 0 1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031432
X-RAY DIFFRACTIONf_angle_d0.6221950
X-RAY DIFFRACTIONf_dihedral_angle_d14.72191
X-RAY DIFFRACTIONf_chiral_restr0.045211
X-RAY DIFFRACTIONf_plane_restr0.006250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.310.36360.264X-RAY DIFFRACTION99.86
4.03-52.970.29451200.26432757X-RAY DIFFRACTION100

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