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- PDB-5oyk: Outer-membrane expressed OmpT of Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 5oyk
TitleOuter-membrane expressed OmpT of Vibrio cholerae
ComponentsGram-negative porin family protein
KeywordsMEMBRANE PROTEIN / Outer membrane protein / Porin / OmpF or OmpC ortholog / ion-transport / membrane beta barrel / ion-channel
Function / homologyGram-negative porin / Porin domain, Gram-negative type / : / Porin domain superfamily / porin activity / pore complex / monoatomic ion transport / cell outer membrane / OmpT protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
Authorsvan den berg, B. / Pathania, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiatives Joint Undertaking115525 United Kingdom
CitationJournal: Structure / Year: 2018
Title: Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae.
Authors: Pathania, M. / Acosta-Gutierrez, S. / Bhamidimarri, S.P. / Basle, A. / Winterhalter, M. / Ceccarelli, M. / van den Berg, B.
History
DepositionSep 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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

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Assembly

Deposited unit
A: Gram-negative porin family protein


Theoretical massNumber of molelcules
Total (without water)35,4251
Polymers35,4251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.610, 74.330, 62.310
Angle α, β, γ (deg.)90.00, 96.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gram-negative porin family protein / OmpT protein / Outer membrane porin-like protein OmpT / Porin


Mass: 35424.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ompT, DN30_688, EN12_08995, ERS013173_00485, ERS013186_03149, ERS013197_04241, ERS013198_02336, ERS013201_00314, ERS013202_01691
Plasmid: pBAD24 / Details (production host): arabinose-inducible promoter / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Omp8 / References: UniProt: O86021

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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: 4.37 Å3/Da / Density meas: 664711.67 Mg/m3 / Density % sol: 72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 15% PEG 4000 0.1 M sodium acetate 0.4 M ammonium thiocyanate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→46.41 Å / Num. obs: 6356 / % possible obs: 98 % / Redundancy: 3.6 % / Net I/av σ(I): 0.9 / Net I/σ(I): 5
Reflection shellHighest resolution: 3.2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.5 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EHD

6ehd


Resolution: 3.2→46.41 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.863 / SU B: 18.991 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24435 323 4.9 %RANDOM
Rwork0.21227 ---
obs0.21381 6206 59.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.525 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å2-0 Å2-1.21 Å2
2---2.68 Å20 Å2
3---5.38 Å2
Refinement stepCycle: 1 / Resolution: 3.2→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 0 0 2467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022521
X-RAY DIFFRACTIONr_bond_other_d0.0020.022190
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9363420
X-RAY DIFFRACTIONr_angle_other_deg0.9335071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9275317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71824.96125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98315380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.914157
X-RAY DIFFRACTIONr_chiral_restr0.080.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02555
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5867.7371274
X-RAY DIFFRACTIONr_mcbond_other4.5877.7381273
X-RAY DIFFRACTIONr_mcangle_it7.65411.5871589
X-RAY DIFFRACTIONr_mcangle_other7.65111.5861590
X-RAY DIFFRACTIONr_scbond_it4.1068.111247
X-RAY DIFFRACTIONr_scbond_other4.1068.111247
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.92112.031831
X-RAY DIFFRACTIONr_long_range_B_refined11.33588.9532869
X-RAY DIFFRACTIONr_long_range_B_other11.33388.9552870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.198→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree1.129 2 -
Rwork0.298 93 -
obs--11.52 %

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