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- PDB-2mlh: NMR Solution Structure of Opa60 from N. Gonorrhoeae in FC-12 Micelles -

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Basic information

Entry
Database: PDB / ID: 2mlh
TitleNMR Solution Structure of Opa60 from N. Gonorrhoeae in FC-12 Micelles
ComponentsOpacity protein opA60
KeywordsMEMBRANE PROTEIN / BETA-BARREL
Function / homologyPorin, opacity type / Opacity family porin protein / Outer membrane autotransporter barrel / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / porin activity / Cell surface interactions at the vascular wall / cell outer membrane / Opacity protein opA60
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model19
AuthorsFox, D.A. / Larsson, P. / Lo, R.H. / Kroncke, B.M. / Kasson, P.M. / Columbus, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Structure of the neisserial outer membrane protein opa60: loop flexibility essential to receptor recognition and bacterial engulfment.
Authors: Fox, D.A. / Larsson, P. / Lo, R.H. / Kroncke, B.M. / Kasson, P.M. / Columbus, L.
History
DepositionFeb 27, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Opacity protein opA60


Theoretical massNumber of molelcules
Total (without water)27,1151
Polymers27,1151
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)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Opacity protein opA60


Mass: 27115.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: MS11 / Gene: opaH / Production host: neisseria gonorrhoeae (bacteria) / References: UniProt: Q04884

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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 HN(COCA)CB
1313D HN(CA)CB
1413D HNCO
1513D HNCA
1613D 1H-15N NOESY
1713D HN(CO)CA
1813D HN(CA)CO

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Sample preparation

DetailsContents: 800 uM [U-100% 13C; U-100% 15N; U-80% 2H] OPA60, 150 mM Dodecyl Phosphcholine, 20 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
800 uMOPA60-1[U-100% 13C; U-100% 15N; U-80% 2H]1
150 mMDodecyl Phosphcholine-21
20 mMsodium phosphate-31
150 mMsodium chloride-41
Sample conditionspH: 6.2 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.31Schwieters, Kuszewski, Tjandra and Clorestructure solution
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
NMRPipe7.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
TopSpin3Bruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 64 / Protein psi angle constraints total count: 64
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 1.5 Å / Maximum upper distance constraint violation: 6.5 Å
NMR ensemble rmsDistance rms dev: 0.11 Å / Distance rms dev error: 0.002 Å

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