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- PDB-5mtf: A modular route to novel potent and selective inhibitors of rhomb... -

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Basic information

Entry
Database: PDB / ID: 5mtf
TitleA modular route to novel potent and selective inhibitors of rhomboid intramembrane proteases
Components
  • Rhomboid protease GlpG
  • inhibitor
KeywordsHYDROLASE / Rhomboid protease / specificity / inhibition / ketoamide
Function / homology
Function and homology information


rhomboid protease / serine-type endopeptidase activity / proteolysis / 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
Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli O45:K1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsTicha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D. / Bachovchin, D. ...Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D. / Bachovchin, D. / Lepsik, M. / Majer, P. / Strisovsky, K.
CitationJournal: Cell Chem Biol / Year: 2017
Title: General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases.
Authors: Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Began, J. / Skerle, J. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D.C. / Bachovchin, D.A. / ...Authors: Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Began, J. / Skerle, J. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D.C. / Bachovchin, D.A. / Lepsik, M. / Majer, P. / Strisovsky, K.
History
DepositionJan 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: 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
C: inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9309
Polymers22,3282
Non-polymers1,6037
Water1,22568
1
A: Rhomboid protease GlpG
C: inhibitor
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)143,58354
Polymers133,96512
Non-polymers9,61742
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area32290 Å2
ΔGint-281 kcal/mol
Surface area43680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.365, 111.365, 124.539
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: 21513.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: glpG, ECS88_3813 / Plasmid: pET25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: B7MDQ0, rhomboid protease
#2: Protein/peptide inhibitor


Mass: 814.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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.: 5
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3M NH4Cl, 25mM Bis Tris pH7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918408 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918408 Å / Relative weight: 1
ReflectionResolution: 1.787→44.97 Å / Num. obs: 28202 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 37.88 Å2 / Net I/σ(I): 18.64
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 4.95 % / Mean I/σ(I) obs: 1.86 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.505
Highest resolutionLowest resolution
Rotation44.97 Å2.14 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QNZ

4qnz


Resolution: 1.79→44.97 Å / SU B: 4.53 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1411 5 %RANDOM
Rwork0.167 ---
obs0.169 26791 99.8 %-
Displacement parametersBiso mean: 35.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.79→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 80 68 1636

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