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- PDB-2xow: Structure of GlpG in complex with a mechanism-based isocoumarin i... -

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Basic information

Entry
Database: PDB / ID: 2xow
TitleStructure of GlpG in complex with a mechanism-based isocoumarin inhibitor
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
5-AMINO-2-(2-METHOXY-2-OXOETHYL)BENZOIC ACID / Rhomboid protease GlpG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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

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Assembly

Deposited unit
A: RHOMBOID PROTEASE GLPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,32618
Polymers20,2141
Non-polymers5,11217
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.690, 110.690, 122.151
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: 20214.020 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 92-270
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: Chemical ChemComp-ISM / 5-AMINO-2-(2-METHOXY-2-OXOETHYL)BENZOIC ACID


Mass: 209.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11NO4
#3: 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.: 16
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMETHYL-2(2-CARBOXY-4-AMINO-PHENYL)ACETATE (ISM): LINKS C1 OF ISM AND OG OF S201 AND C8 OF ISM AND ...METHYL-2(2-CARBOXY-4-AMINO-PHENYL)ACETATE (ISM): LINKS C1 OF ISM AND OG OF S201 AND C8 OF ISM AND NE2 OF H254 THE ISOCOUMARIN RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 ON C1-O1 BOND AND SUBSEQUENTLY A REACTION BETWEEN HISTIDINE AT THE ACTIVE SITE CREATES A SECOND COVALENT BOND. ISM IS IDENTICAL TO HETEROGEN ICU IN PDB 1JIM BUT LACKS AN ACETATE MOLECULE AT POSITION C8. DIFFERENCE MAP PEAK INDICATE A POSSIBILITY OF ALTERNATE CONFORMATION AT RESIDUES 250-252 BUT SINCE THE DENSITY IS WEAK ONLY ONE CONFORMATION BASED ON GEOMETRY AND MAP HAS BEEN MODELLED. THE OCCUPANCY OF THE LIGAND ISM IS SET TO 1, WHEN REFINED IT INDICATES AN OCCUPANCY OF 0.92-0.96.

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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: 63.47 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2 M AMMONIUM CHLORIDE, 0.1 M BIS-TRIS PH 7.0, 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.09→44.62 Å / Num. obs: 16662 / % possible obs: 97 % / Redundancy: 4.9 % / Biso Wilson estimate: 37.61 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.9 / % possible all: 85.4

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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: 2.09→31.161 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 23.42 / Stereochemistry target values: ML
Details: COVALENT LINK OF ICM WITH OG OF SER 201 AND NE2 OF HIS 254
RfactorNum. reflection% reflection
Rfree0.2429 844 5.1 %
Rwork0.1982 --
obs0.2004 16657 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.419 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 44.72 Å2
Baniso -1Baniso -2Baniso -3
1--6.6529 Å20 Å20 Å2
2---6.6529 Å20 Å2
3---13.3058 Å2
Refinement stepCycle: LAST / Resolution: 2.09→31.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 142 38 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071604
X-RAY DIFFRACTIONf_angle_d1.1192136
X-RAY DIFFRACTIONf_dihedral_angle_d14.301571
X-RAY DIFFRACTIONf_chiral_restr0.059221
X-RAY DIFFRACTIONf_plane_restr0.004242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.22090.2761280.24872273X-RAY DIFFRACTION85
2.2209-2.39230.26751540.21692608X-RAY DIFFRACTION97
2.3923-2.6330.23551370.19852707X-RAY DIFFRACTION100
2.633-3.01370.26211500.18952715X-RAY DIFFRACTION100
3.0137-3.79590.2191460.18462738X-RAY DIFFRACTION100
3.7959-31.16460.24081290.19872772X-RAY DIFFRACTION98

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