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- PDB-5onu: Trimeric OmpU structure -

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Basic information

Entry
Database: PDB / ID: 5onu
TitleTrimeric OmpU structure
ComponentsOuter membrane protein OmpU
KeywordsMEMBRANE PROTEIN / Outer membrane protein / Bacterial outer membrane protein / OmpU / Vibrio cholerae / invasion
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Gram-negative porin / Porin domain, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
: / Outer membrane protein U
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsLi, H.Y. / Dong, C.J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structure of the outer membrane protein OmpU from Vibrio cholerae at 2.2 angstrom resolution.
Authors: Li, H. / Zhang, W. / Dong, C.
History
DepositionAug 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 19, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_symm_contact / struct_conn
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein OmpU
B: Outer membrane protein OmpU
C: Outer membrane protein OmpU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,32622
Polymers115,5603
Non-polymers3,76619
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19090 Å2
ΔGint-15 kcal/mol
Surface area42170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.880, 153.470, 81.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Outer membrane protein OmpU


Mass: 38519.902 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: B2J67_03320, B2J68_03135, B2J70_03210, B2J71_03065, BTY66_11390, CEF09_10965
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1_S (others)
Variant (production host): C43 / References: UniProt: A0A1V9N7P1, UniProt: P0C6Q6*PLUS
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M lithium sulfate monohydrate, 0.1M sodium acetate trihydrate pH4.6, and 1M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 146 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K-W / Detector: PIXEL / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.22→64.95 Å / Num. obs: 80557 / % possible obs: 99.8 % / Redundancy: 8.3 % / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→62.731 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 4019 4.99 %RANDOM
Rwork0.2078 ---
obs0.2092 80484 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→62.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 259 637 8240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047716
X-RAY DIFFRACTIONf_angle_d1.00210355
X-RAY DIFFRACTIONf_dihedral_angle_d17.9222798
X-RAY DIFFRACTIONf_chiral_restr0.0361053
X-RAY DIFFRACTIONf_plane_restr0.0031359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.24610.30451210.31872614X-RAY DIFFRACTION99
2.2461-2.27350.33131340.3162537X-RAY DIFFRACTION99
2.2735-2.30230.3221400.31012592X-RAY DIFFRACTION98
2.3023-2.33260.34971220.29052592X-RAY DIFFRACTION99
2.3326-2.36460.35231300.28022620X-RAY DIFFRACTION100
2.3646-2.39830.28961390.26772612X-RAY DIFFRACTION100
2.3983-2.43410.30761400.26072604X-RAY DIFFRACTION100
2.4341-2.47220.26441480.24532599X-RAY DIFFRACTION100
2.4722-2.51270.28921450.24542601X-RAY DIFFRACTION100
2.5127-2.5560.28251300.23882634X-RAY DIFFRACTION100
2.556-2.60250.26731310.22952622X-RAY DIFFRACTION100
2.6025-2.65260.25521400.22622592X-RAY DIFFRACTION100
2.6526-2.70670.26521400.22482633X-RAY DIFFRACTION100
2.7067-2.76560.24081430.21632615X-RAY DIFFRACTION100
2.7656-2.82990.27121310.20292627X-RAY DIFFRACTION100
2.8299-2.90070.22721250.22062663X-RAY DIFFRACTION100
2.9007-2.97910.22471210.20562614X-RAY DIFFRACTION100
2.9791-3.06680.24871250.2122645X-RAY DIFFRACTION100
3.0668-3.16570.2561490.22282615X-RAY DIFFRACTION100
3.1657-3.27890.24351530.22292645X-RAY DIFFRACTION100
3.2789-3.41020.28191360.20592648X-RAY DIFFRACTION100
3.4102-3.56540.21081550.19412620X-RAY DIFFRACTION100
3.5654-3.75330.22171490.18332642X-RAY DIFFRACTION100
3.7533-3.98840.21081340.18662660X-RAY DIFFRACTION100
3.9884-4.29630.20421430.1772672X-RAY DIFFRACTION100
4.2963-4.72850.18181430.16132677X-RAY DIFFRACTION100
4.7285-5.41240.17661460.16832706X-RAY DIFFRACTION100
5.4124-6.81780.22881670.19392703X-RAY DIFFRACTION100
6.8178-62.75620.24581390.22152861X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -26.1797 Å / Origin y: 2.0739 Å / Origin z: -3.5018 Å
111213212223313233
T0.2002 Å20.0059 Å2-0.0015 Å2-0.2332 Å20.0087 Å2--0.2307 Å2
L0.1246 °2-0.0181 °20.0552 °2-0.3756 °20.0301 °2--0.1643 °2
S-0.0174 Å °0.0142 Å °0.0032 Å °0.0032 Å °0.0113 Å °-0.0216 Å °0.0113 Å °0.0298 Å °-0 Å °
Refinement TLS groupSelection details: all

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