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

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Basic information

Entry
Database: PDB / ID: 3zmh
TitleStructure of E.coli rhomboid protease GlpG in complex with monobactam L62
ComponentsRHOMBOID PROTEASE GLPG
KeywordsHYDROLASE / INTRA-MEMBRANE PROTEASE / ACYL ENZYME / BETA LACTAMS / ANITBIOTIC
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 domain / Rhomboid-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CYCLOPENTYL 2-OXO-4-PHENYLAZETIDINE-1-CARBOXYLATE / Chem-L62 / Rhomboid protease GlpG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 11, 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 / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _citation.journal_id_ISSN / _citation.page_last ..._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 / _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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)22,77311
Polymers20,3431
Non-polymers2,43010
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)110.150, 110.150, 128.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein / Sugars , 2 types, 7 molecules A

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


Mass: 20343.133 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 91-270
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
#4: 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.: 6
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 42 molecules

#2: Chemical ChemComp-L62 / cyclopentyl N-[(1R)-3-oxidanylidene-1-phenyl-propyl]carbamate


Mass: 261.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19NO3
#3: Chemical ChemComp-78C / CYCLOPENTYL 2-OXO-4-PHENYLAZETIDINE-1-CARBOXYLATE


Mass: 259.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17NO3
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsCYCLOPENTYL (1-PHENYLBUT-3-EN-1YL)CARBAMATE (L62): L62 IS 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: 3.56 Å3/Da / Density % sol: 65.6 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M NACL, 0.1M BIS-TRIS PH7.0, 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9687
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.3→76.62 Å / Num. obs: 13547 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 34.18 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

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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 2XOV

2xov


Resolution: 2.3→76.622 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 21.76 / Stereochemistry target values: ML
Details: BNG 405 IS IN SPECIAL POSITION. L62 IS COVALENTLY LINKED TO S201. EXTERNAL RESTRAINTS USED BETWEEN C2 OF 401 AND CL 409. A RACEMIC MIXTURE OF L62 WAS USED IN THE SOAKS. NOTE THAT THE ...Details: BNG 405 IS IN SPECIAL POSITION. L62 IS COVALENTLY LINKED TO S201. EXTERNAL RESTRAINTS USED BETWEEN C2 OF 401 AND CL 409. A RACEMIC MIXTURE OF L62 WAS USED IN THE SOAKS. NOTE THAT THE EXTERNALLY BOUND BETA LACTAM HAS THE OPPOSITE CHIRALITY OF THE BETA LACTAM BOUND TO S201.
RfactorNum. reflection% reflection
Rfree0.2288 672 5 %
Rwork0.1881 --
obs0.19 13542 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→76.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1425 0 81 38 1544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071576
X-RAY DIFFRACTIONf_angle_d1.0222132
X-RAY DIFFRACTIONf_dihedral_angle_d12.069541
X-RAY DIFFRACTIONf_chiral_restr0.075225
X-RAY DIFFRACTIONf_plane_restr0.004247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.47760.24471420.20112551X-RAY DIFFRACTION100
2.4776-2.7270.21731350.17552526X-RAY DIFFRACTION100
2.727-3.12160.24461450.16672529X-RAY DIFFRACTION100
3.1216-3.93280.21541170.17912602X-RAY DIFFRACTION100
3.9328-76.66420.2291330.20242662X-RAY DIFFRACTION100

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