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- PDB-2o7l: The open-cap conformation of GlpG -

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Basic information

Entry
Database: PDB / ID: 2o7l
TitleThe open-cap conformation of GlpG
ComponentsProtein glpG
KeywordsMEMBRANE PROTEIN / intramembrane proteolysis / rhomboid protease / GlpG
Function / homology
Function and homology information


rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Rhomboid-like fold / Rhomboid-like / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHa, Y.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Open-cap conformation of intramembrane protease GlpG.
Authors: Wang, Y. / Ha, Y.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein glpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5482
Polymers20,2421
Non-polymers3061
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.4, 111.4, 128.6
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Protein glpG


Mass: 20242.008 Da / Num. of mol.: 1 / Fragment: core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09391
#2: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3M NaCl, 100mM Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorDetector: CCD / Date: Oct 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 10493 / % possible obs: 96.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1038 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IC8

2ic8


Resolution: 2.5→40 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1049 -random
Rwork0.24 ---
obs-10493 96.8 %-
Displacement parametersBiso mean: 41.871 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 21 40 1456

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