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- PDB-6ehc: OmpUdeltaN (N-terminus deletion mutant of OmpU), outer membrane p... -

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Basic information

Entry
Database: PDB / ID: 6ehc
TitleOmpUdeltaN (N-terminus deletion mutant of OmpU), 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: 2.02 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,34912
Polymers67,2852
Non-polymers3,06410
Water4,612256
1
A: Outer membrane protein U
hetero molecules

A: Outer membrane protein U
hetero molecules

A: Outer membrane protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,44321
Polymers100,9273
Non-polymers5,51618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
B: Outer membrane protein U
hetero molecules

B: Outer membrane protein U
hetero molecules

B: Outer membrane protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,60515
Polymers100,9273
Non-polymers3,67712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)81.360, 81.360, 198.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-404-

C8E

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Components

#1: Protein Outer membrane protein U / Porin OmpU


Mass: 33642.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a N-terminal deletion mutant (first 10 resdiues deleted) of OmpU (OM porin) of Vibrio cholerae.
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: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5F934
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.71 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 33% PEG 300, 0.1 M NaCl, 0.05 M bicine

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.02→57.52 Å / Num. obs: 48646 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.9 / Net I/σ(I): 12.3
Reflection shellHighest resolution: 2.02 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EHB

6ehb


Resolution: 2.02→57.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.9 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24761 2419 5 %RANDOM
Rwork0.1926 ---
obs0.19533 46172 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.774 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å2-0.87 Å20 Å2
2---1.74 Å20 Å2
3---5.64 Å2
Refinement stepCycle: 1 / Resolution: 2.02→57.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 97 256 5067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.024902
X-RAY DIFFRACTIONr_bond_other_d0.0020.024323
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9526585
X-RAY DIFFRACTIONr_angle_other_deg0.943310016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9675614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65524.883256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12415737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.41522
X-RAY DIFFRACTIONr_chiral_restr0.1090.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021075
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_it3.0113.8192456
X-RAY DIFFRACTIONr_mcbond_other3.0093.8192455
X-RAY DIFFRACTIONr_mcangle_it4.2095.6973062
X-RAY DIFFRACTIONr_mcangle_other4.2095.6973063
X-RAY DIFFRACTIONr_scbond_it3.6364.2412446
X-RAY DIFFRACTIONr_scbond_other3.6364.2412447
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3926.193520
X-RAY DIFFRACTIONr_long_range_B_refined7.16443.0314923
X-RAY DIFFRACTIONr_long_range_B_other7.16443.0394924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.073 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 209 -
Rwork0.301 3403 -
obs--100 %

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