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- PDB-2lhf: Solution structure of outer membrane protein H (OprH) from P. aer... -

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Basic information

Entry
Database: PDB / ID: 2lhf
TitleSolution structure of outer membrane protein H (OprH) from P. aeruginosa in DHPC micelles
ComponentsOuter membrane protein H1
KeywordsMEMBRANE PROTEIN / beta-barrel
Function / homologyPorin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta / Outer membrane beta-barrel protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 15
AuthorsEdrington, T.C.V. / Tamm, L.K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for the Interaction of Lipopolysaccharide with Outer Membrane Protein H (OprH) from Pseudomonas aeruginosa.
Authors: Edrington, T.C. / Kintz, E. / Goldberg, J.B. / Tamm, L.K.
History
DepositionAug 8, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Atomic model
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Nov 30, 2011Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5May 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: Outer membrane protein H1


Theoretical massNumber of molelcules
Total (without water)19,5491
Polymers19,5491
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Outer membrane protein H1 / PhoP/Q and low Mg2+ inducible outer membrane protein H1


Mass: 19549.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: oprH, PA1178 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51486

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC-TROSY
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D HN(COCA)CB
1613D HNCO
1713D HCACO
1813D 1H-15N NOESY-TROSY
1913D 1H-15N NOESY-TROSY-NOESY

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Sample preparation

DetailsContents: 25 mM [U-13C; U-15N; U-2H] sodium phosphate, 50 mM [U-13C; U-15N; U-2H] potassium chloride, 0.05 % [U-13C; U-15N; U-2H] sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphate-1[U-13C; U-15N; U-2H]1
50 mMpotassium chloride-2[U-13C; U-15N; U-2H]1
0.05 %sodium azide-3[U-13C; U-15N; U-2H]1
Sample conditionspH: 6.1 / Pressure: ambient / Temperature: 315 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 4,000 high temperature, 8,000 torsion slow-cool, and 8,000 cartesian slow-cool annealing steps.
NMR constraintsNOE constraints total: 199 / NOE intraresidue total count: 0 / NOE long range total count: 95 / NOE medium range total count: 11 / NOE sequential total count: 93 / Hydrogen bond constraints total count: 134 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 94 / Protein psi angle constraints total count: 94
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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