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- PDB-2n2m: NMR structure of yersinia pestis Ail (attachment invasion locus) ... -

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Basic information

Entry
Database: PDB / ID: 2n2m
TitleNMR structure of yersinia pestis Ail (attachment invasion locus) in decylphosphocholine micelles
ComponentsOuter membrane protein X
KeywordsMEMBRANE PROTEIN
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 speciesYersinia pestis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsMarassi, F.M. / Ding, Y. / Yao, Y.
CitationJournal: J.Biomol.Nmr / Year: 2015
Title: Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.
Authors: Marassi, F.M. / Ding, Y. / Schwieters, C.D. / Tian, Y. / Yao, Y.
History
DepositionMay 10, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Outer membrane protein X


Theoretical massNumber of molelcules
Total (without water)17,4921
Polymers17,4921
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 #1lowest energy

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Components

#1: Protein Outer membrane protein X


Mass: 17492.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ompX, y1324 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q8D0Z7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.4-0.5 mM [U-100% 13C; U-100% 15N] Yersinia pestis Ail, 20 mM sodium phosphate, 5 mM sodium chloride, 170 mM decyl-phosphocholine (DePC), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMYersinia pestis Ail-1[U-100% 13C; U-100% 15N]0.4-0.51
20 mMsodium phosphate-21
5 mMsodium chloride-31
170 mMdecyl-phosphocholine (DePC)-41
Sample conditionsIonic strength: 25 / pH: 6.8 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxchemical shift calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were folded and refined using the standard nonbonded potential REPEL
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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