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- PDB-6ehb: OmpU, an outer membrane protein, of Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6ehb
TitleOmpU, an outer membrane protein, of Vibrio cholerae
ComponentsOuter membrane protein U
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 / pore complex / monoatomic ion transport / cell outer membrane / Outer membrane protein U
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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: Outer membrane protein U
B: Outer membrane protein U
C: Outer membrane protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,10826
Polymers104,0603
Non-polymers7,04823
Water11,512639
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19110 Å2
ΔGint24 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.723, 153.840, 66.170
Angle α, β, γ (deg.)90.00, 102.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer membrane protein U / Porin OmpU


Mass: 34686.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: ompU, VC0395_A0162, VC395_0650 / Plasmid: pBAD24a / Details (production host): arabinose inducible promoter / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Omp8 / References: UniProt: A5F934
#2: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M sodium acetate, 0.1 M MES, 28% w/v 400 PEG

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.55→49.49 Å / Num. obs: 171689 / % possible obs: 97 % / Redundancy: 3.9 % / CC1/2: 0.9 / Rpim(I) all: 0.037 / Net I/σ(I): 9.8
Reflection shellHighest resolution: 1.55 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.5 / Rpim(I) all: 0.555 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPG

3upg


Resolution: 1.55→49.49 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.5 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19929 8445 4.9 %RANDOM
Rwork0.17029 ---
obs0.17172 163191 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.584 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0.03 Å2
2---0.45 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.55→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7301 0 202 639 8142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.027656
X-RAY DIFFRACTIONr_bond_other_d0.0020.026773
X-RAY DIFFRACTIONr_angle_refined_deg2.1491.95610268
X-RAY DIFFRACTIONr_angle_other_deg1.046315689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84725.025396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.967151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5891533
X-RAY DIFFRACTIONr_chiral_restr0.1340.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021653
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_it2.2852.0673832
X-RAY DIFFRACTIONr_mcbond_other2.2842.0673831
X-RAY DIFFRACTIONr_mcangle_it3.1193.0914786
X-RAY DIFFRACTIONr_mcangle_other3.1193.0914787
X-RAY DIFFRACTIONr_scbond_it3.5662.583824
X-RAY DIFFRACTIONr_scbond_other3.5652.5813825
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2843.6565477
X-RAY DIFFRACTIONr_long_range_B_refined6.55925.4218346
X-RAY DIFFRACTIONr_long_range_B_other6.55925.4268347
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 586 -
Rwork0.274 11813 -
obs--95.08 %

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