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- PDB-2gqc: Solution structure of the N-terminal domain of Rhomboid Intramemb... -

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Basic information

Entry
Database: PDB / ID: 2gqc
TitleSolution structure of the N-terminal domain of Rhomboid Intramembrane Protease from P. aeruginosa
ComponentsRhomboid Intramembrane Protease
KeywordsHYDROLASE / alpha-beta domain
Function / homology
Function and homology information


serine-type endopeptidase activity / membrane
Similarity search - Function
Alpha-Beta Plaits - #2080 / Rhomboid protease, N-terminal / Rhomboid protease, N-terminal domain superfamily / Rhomboid N-terminal domain / Peptidase S54, rhomboid domain / Rhomboid family / Rhomboid-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Rhomboid family intramembrane serine protease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing torsional angle dynamics
AuthorsDutta, K. / Del Rio, A. / Chavez, J. / Ubarretxena-Belandia, I. / Ghose, R.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution structure and dynamics of the N-terminal cytosolic domain of rhomboid intramembrane protease from Pseudomonas aeruginosa: insights into a functional role in intramembrane proteolysis.
Authors: Del Rio, A. / Dutta, K. / Chavez, J. / Ubarretxena-Belandia, I. / Ghose, R.
History
DepositionApr 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid Intramembrane Protease


Theoretical massNumber of molelcules
Total (without water)7,9411
Polymers7,9411
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 / 1500structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Rhomboid Intramembrane Protease


Mass: 7941.021 Da / Num. of mol.: 1 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: pET 15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: GenBank: 9949195, UniProt: Q9HZC2*PLUS, rhomboid protease

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
NMR detailsText: This structure was determined using standard 2D and 3D heteronuclear techniques.

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Sample preparation

DetailsContents: 1 mM, U-15N,13C; 20 mM Bis-Tris, 50 mM NaCl pH 6.5
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionClassification
NMRPipeprocessing
NMRView5.2.2data analysis
ARIA2structure solution
CNS1.1refinement
RefinementMethod: simulated annealing torsional angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1500 / Conformers submitted total number: 20

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