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- PDB-6ehe: OmpTdeltaL8 (loop L8 deletion mutant of OmpT), an outer membrane ... -

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Basic information

Entry
Database: PDB / ID: 6ehe
TitleOmpTdeltaL8 (loop L8 deletion mutant of OmpT), an outer membrane protein of Vibrio cholerae
ComponentsOmpT protein
KeywordsMEMBRANE PROTEIN / Outer membrane protein / Porin / OmpF or OmpC ortholog / ion-transport / membrane beta barrel / ion-channel / diffusion porin / diffusion channel / non-specific porin.
Function / homologyGram-negative porin / Porin domain, Gram-negative type / Porin domain superfamily / porin activity / cell outer membrane / metal ion binding / ACETATE ION / OmpT protein
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.312 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 13, 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 1.2Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Jan 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: OmpT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,33412
Polymers34,7401
Non-polymers2,59411
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint13 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.480, 128.410, 171.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein OmpT protein


Mass: 34739.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: OmpTdeltaL8 is 18 residue deletion from the L8 loop of OmpT (Thr294 to Thr309, in mature sequence).
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Gene: ompT, VC0395_A1445 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AME7
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.05 magnesium acetate, 0.1 M glycine, 32% PEG 400

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.31→85.84 Å / Num. obs: 18688 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.9 / Rpim(I) all: 0.034 / Net I/σ(I): 13.1
Reflection shellHighest resolution: 2.31 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.6 / Rpim(I) all: 0.51 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EHD

6ehd


Resolution: 2.312→52.271 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.34
RfactorNum. reflection% reflection
Rfree0.273 905 4.84 %
Rwork0.2247 --
obs0.2269 18684 86.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.312→52.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 86 39 2460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112472
X-RAY DIFFRACTIONf_angle_d1.1133320
X-RAY DIFFRACTIONf_dihedral_angle_d10.4661884
X-RAY DIFFRACTIONf_chiral_restr0.065341
X-RAY DIFFRACTIONf_plane_restr0.006429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.312-2.45690.2792740.21551378X-RAY DIFFRACTION41
2.4569-2.64650.31411390.25682629X-RAY DIFFRACTION78
2.6465-2.91290.30531650.25023395X-RAY DIFFRACTION99
2.9129-3.33430.30851570.24773386X-RAY DIFFRACTION99
3.3343-4.20060.26581740.21243419X-RAY DIFFRACTION99
4.2006-52.28420.24831960.21333572X-RAY DIFFRACTION100

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