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- PDB-2irv: Crystal structure of GlpG, a rhomboid intramembrane serine protease -

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Basic information

Entry
Database: PDB / ID: 2irv
TitleCrystal structure of GlpG, a rhomboid intramembrane serine protease
ComponentsProtein glpG
KeywordsMEMBRANE PROTEIN / cavity / ser-his dyad
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
Chem-PGV / PHOSPHATE ION / Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.3 Å
AuthorsBibi, E. / Fass, D. / Ben-Shem, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for intramembrane proteolysis by rhomboid serine proteases.
Authors: Ben-Shem, A. / Fass, D. / Bibi, E.
History
DepositionOct 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein glpG
B: Protein glpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,38524
Polymers41,1132
Non-polymers7,27222
Water1,45981
1
A: Protein glpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2454
Polymers20,5561
Non-polymers6883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein glpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,14020
Polymers20,5561
Non-polymers6,58419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.820, 69.350, 67.580
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Protein glpG


Mass: 20556.393 Da / Num. of mol.: 2 / Fragment: protease core, residues 92-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glpG / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P09391
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 102 molecules

#2: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 30% PEG 400, 200 mM CaCl2 in reservoir, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17028 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Redundancy: 3 % / Rsym value: 0.081 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.411 / % possible all: 97.2

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.263 1175 random
Rwork0.22 --
obs-17028 -
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 290 81 3196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.301

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