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- PDB-2lep: Solution Structure of N-terminal Cytosolic Domain of Rhomboid Int... -

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Basic information

Entry
Database: PDB / ID: 2lep
TitleSolution Structure of N-terminal Cytosolic Domain of Rhomboid Intramembrane Protease from Escherichia Coli
ComponentsRhomboid protease glpG 1
KeywordsHYDROLASE / Cell Membrane / Cytosol / Membrane Protein / Micelles / Serine Protease / Domain Swapping
Function / homology
Function and homology information


rhomboid protease / endopeptidase activity / membrane => GO:0016020 / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2350 / Peptidase S54, GlpG peptidase, N-terminal / Rhomboid protease GlpG / GlpG peptidase, N-terminal domain superfamily / Cytoplasmic N-terminal domain of rhomboid serine protease / Peptidase S54, rhomboid domain / Rhomboid family / Rhomboid-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Rhomboid protease GlpG / Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsSherratt, A.R. / Ghasriani, H. / Goto, N.K.
CitationJournal: Biochemistry / Year: 2012
Title: Activity-Based Protein Profiling of the Escherichia coli GlpG Rhomboid Protein Delineates the Catalytic Core.
Authors: Sherratt, A.R. / Blais, D.R. / Ghasriani, H. / Pezacki, J.P. / Goto, N.K.
History
DepositionJun 20, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid protease glpG 1


Theoretical massNumber of molelcules
Total (without water)7,9711
Polymers7,9711
Non-polymers00
Water0
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 Rhomboid protease glpG 1 / Intramembrane serine protease 1


Mass: 7970.885 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG1, ECs4267 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: C3SPT7, UniProt: P09391*PLUS, rhomboid protease

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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 HNCO
1313D HNCA
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D HN(CO)CA
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1923D 1H-13C NOESY aliphatic
11023D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] Nglpg, 25mM NaH2PO4, 150mM NaCl, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] Nglpg, 25mM NaH2PO4, 150mM NaCl, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMNglpg-1[U-100% 13C; U-100% 15N]1
1.0 mMNglpg-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.30 M NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR_NIH2.22Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Explicit solvent refinement.
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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