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- PDB-3zot: Structure of E.coli rhomboid protease GlpG in complex with monoba... -

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Basic information

Entry
Database: PDB / ID: 3zot
TitleStructure of E.coli rhomboid protease GlpG in complex with monobactam L29 (data set 2)
ComponentsRHOMBOID PROTEASE GLPG
KeywordsHYDROLASE / INTRA-MEMBRANE PROTEASE / ACYL ENZYME / BETA LACTAMS / ANTIBIOTIC
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-L6C / Rhomboid protease GlpG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.399 Å
AuthorsVinothkumar, K.R. / Pierrat, O.A. / Large, J.M. / Freeman, M.
CitationJournal: Structure / Year: 2013
Title: Structure of Rhomboid Protease in Complex with Beta-Lactam Inhibitors Defines the S2' Cavity.
Authors: Vinothkumar, K.R. / Pierrat, O.A. / Large, J.M. / Freeman, M.
History
DepositionFeb 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
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_conn / 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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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)23,42613
Polymers20,3281
Non-polymers3,09812
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.200, 110.200, 128.900
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


Mass: 20328.121 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 92-271
Source method: isolated from a genetically manipulated source
Details: THE BETA LACTAM RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 ON C2-O1 TO FORM A COVALENT BOND
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P09391, rhomboid protease
#2: Chemical ChemComp-L6C / phenyl N-[(1R)-3-oxidanylidene-1-phenyl-propyl]carbamate


Mass: 269.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15NO3
#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.: 9
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPHENYL(1-PHENYLBUT-3-EN-1-YL)CARBAMATE (L6C): COVALENTLY BONDED TO S201

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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: 3.52 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.25M NH4CL, 0.1M BIS-TRIS, PH7.0, 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→53.4 Å / Num. obs: 11901 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 37.14 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOV

2xov


Resolution: 2.399→53.379 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 24.79 / Stereochemistry target values: ML
Details: BNG 406 IS ON SPECIAL POSITION AND REFINED WITH 0.5 OCCUPANCY. RESIDUES 248 AND 249 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2517 582 4.9 %
Rwork0.1984 --
obs0.2008 11900 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.9 Å2
Refinement stepCycle: LAST / Resolution: 2.399→53.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 90 29 1530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081553
X-RAY DIFFRACTIONf_angle_d1.0612092
X-RAY DIFFRACTIONf_dihedral_angle_d13.762536
X-RAY DIFFRACTIONf_chiral_restr0.068224
X-RAY DIFFRACTIONf_plane_restr0.005242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3993-2.64070.2851450.21822786X-RAY DIFFRACTION100
2.6407-3.02280.29941640.20072794X-RAY DIFFRACTION100
3.0228-3.80830.25551330.19812858X-RAY DIFFRACTION100
3.8083-53.3920.22181400.19292880X-RAY DIFFRACTION98

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