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- PDB-2mnh: Refined structure of outer membrane protein x in nanodisc by meas... -

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Basic information

Entry
Database: PDB / ID: 2mnh
TitleRefined structure of outer membrane protein x in nanodisc by measuring residual dipolar couplings
ComponentsOuter membrane protein X
KeywordsMEMBRANE PROTEIN / BETA BARREL / RESIDUAL DIPOLAR COUPLING / NANODISC / OMPX
Function / homology
Function and homology information


host outer membrane / cell outer membrane
Similarity search - Function
: / Enterobacterial virulence outer membrane protein signature 1. / Enterobacterial virulence outer membrane protein signature 2. / Virulence-related outer membrane protein / Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Porin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein X / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsBibow, S. / Carneiro, M.G. / Sabo, T.M. / Schwiegk, C. / Becker, S. / Riek, R. / Lee, D.
CitationJournal: Protein Sci. / Year: 2014
Title: Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings.
Authors: Bibow, S. / Carneiro, M.G. / Sabo, T.M. / Schwiegk, C. / Becker, S. / Riek, R. / Lee, D.
History
DepositionApr 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein X


Theoretical massNumber of molelcules
Total (without water)16,3721
Polymers16,3721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Outer membrane protein X


Mass: 16371.768 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: B0814, BN896_0667, JW0799, ompX, YBIG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: U6N4S7, UniProt: P0A917*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D HNCA
1312D 1H-15N HSQC
1412D 1H-15N COCAINE

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] OUTER MEMBRANE PROTEIN X, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: OUTER MEMBRANE PROTEIN X-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 / pH: 7.4 / Pressure: AMBIENT / Temperature: 318 K

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NMR measurement

NMR spectrometerType: BRUKER AVANCE I and AVANCE III / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSCHWIETERS, KUSZEWSKI, TJrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
TopSpinBruker Biospinstructure solution
SparkyGoddardstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 58 / Hydrogen bond constraints total count: 85 / Protein phi angle constraints total count: 97 / Protein psi angle constraints total count: 97
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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