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- PDB-2xov: Crystal Structure of E.coli rhomboid protease GlpG, native enzyme -

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Basic information

Entry
Database: PDB / ID: 2xov
TitleCrystal Structure of E.coli rhomboid protease GlpG, native enzyme
ComponentsRHOMBOID PROTEASE GLPG
KeywordsHYDROLASE / MEMBRANE PROTEIN / INTRAMEMBRANE PROTEASE
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: 1.65 Å
AuthorsVinothkumar, K.R. / Strisovsky, K. / Andreeva, A. / Christova, Y. / Verhelst, S. / Freeman, M.
CitationJournal: EMBO J. / Year: 2010
Title: The structural basis for catalysis and substrate specificity of a rhomboid protease.
Authors: Vinothkumar, K.R. / Strisovsky, K. / Andreeva, A. / Christova, Y. / Verhelst, S. / Freeman, M.
History
DepositionAug 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: RHOMBOID PROTEASE GLPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,37121
Polymers20,4571
Non-polymers5,91420
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.400, 110.400, 127.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein RHOMBOID PROTEASE GLPG / INTRAMEMBRANE SERINE PROTEASE / GLPG


Mass: 20457.234 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 91-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P09391, rhomboid protease
#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.: 19
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.5 Å3/Da / Density % sol: 64.92 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3M AMMONIUM CHLORIDE, 0.1M BIS-TRIS PH7.0, 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→55.2 Å / Num. obs: 36099 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 23.12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B45

3b45


Resolution: 1.65→34.775 Å / SU ML: 0.17 / σ(F): 0.38 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 1794 5 %
Rwork0.1923 --
obs0.1935 36038 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.304 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.883 Å2-0 Å20 Å2
2---0.883 Å20 Å2
3---1.7659 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 204 87 1730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061678
X-RAY DIFFRACTIONf_angle_d12213
X-RAY DIFFRACTIONf_dihedral_angle_d13.008613
X-RAY DIFFRACTIONf_chiral_restr0.067230
X-RAY DIFFRACTIONf_plane_restr0.004244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69460.27511270.26022633X-RAY DIFFRACTION100
1.6946-1.74450.27751510.25032623X-RAY DIFFRACTION100
1.7445-1.80080.26911340.23982599X-RAY DIFFRACTION99
1.8008-1.86520.28511450.21612607X-RAY DIFFRACTION100
1.8652-1.93980.22381410.20412620X-RAY DIFFRACTION100
1.9398-2.02810.20211150.18722628X-RAY DIFFRACTION100
2.0281-2.1350.19171400.18012631X-RAY DIFFRACTION100
2.135-2.26880.19811450.17882613X-RAY DIFFRACTION100
2.2688-2.44390.21341410.18382636X-RAY DIFFRACTION100
2.4439-2.68980.21141450.17782621X-RAY DIFFRACTION100
2.6898-3.07880.20921530.16722641X-RAY DIFFRACTION100
3.0788-3.87810.17931230.16852671X-RAY DIFFRACTION99
3.8781-34.78240.23951340.20742721X-RAY DIFFRACTION98

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