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- PDB-5mt6: Structure of E.coli GlpG in complex with peptide derived inhibito... -

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Basic information

Entry
Database: PDB / ID: 5mt6
TitleStructure of E.coli GlpG in complex with peptide derived inhibitor Ac-RVRHA-phenylethyl-ketoamide
Components
  • ACE-ARG-VAL-ARG-HIS-ALA-V9C
  • Rhomboid 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 K-12 (bacteria)
Providencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsVinothkumar, K.R.
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 6, 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 1.2May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 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 1.5Jan 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
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhomboid protease GlpG
B: ACE-ARG-VAL-ARG-HIS-ALA-V9C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7704
Polymers21,1572
Non-polymers6132
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-5 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.710, 111.710, 124.229
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: 20343.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glpG, b3424, JW5687 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P09391, rhomboid protease
#2: Protein/peptide ACE-ARG-VAL-ARG-HIS-ALA-V9C


Mass: 813.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria)
#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.: 2
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.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 64.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.16→52.31 Å / Num. obs: 16097 / % possible obs: 99.4 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.559 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XOV

2xov


Resolution: 2.16→52.31 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.062 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26593 781 4.9 %RANDOM
Rwork0.21355 ---
obs0.21598 15315 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.458 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å2-0 Å2
2---0.35 Å2-0 Å2
3---1.15 Å2
Refinement stepCycle: 1 / Resolution: 2.16→52.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 22 28 1528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191549
X-RAY DIFFRACTIONr_bond_other_d0.0010.021480
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9382102
X-RAY DIFFRACTIONr_angle_other_deg0.94833373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81121.35659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71615236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.941158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.9513.92740
X-RAY DIFFRACTIONr_mcbond_other6.9433.92739
X-RAY DIFFRACTIONr_mcangle_it7.2965.812921
X-RAY DIFFRACTIONr_mcangle_other7.2965.812922
X-RAY DIFFRACTIONr_scbond_it9.2734.684809
X-RAY DIFFRACTIONr_scbond_other9.2674.687810
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.0566.7381182
X-RAY DIFFRACTIONr_long_range_B_refined12.75346.9541851
X-RAY DIFFRACTIONr_long_range_B_other12.74846.9491850
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 63 -
Rwork0.342 1114 -
obs--99.66 %
Refinement TLS params.Method: refined / Origin x: -17.7033 Å / Origin y: 7.8982 Å / Origin z: -43.7712 Å
111213212223313233
T0.0287 Å20.0092 Å20.0067 Å2-0.0631 Å2-0.0056 Å2--0.0076 Å2
L0.7471 °2-0.1257 °20.2846 °2-0.1707 °2-0.0021 °2--0.601 °2
S-0.0123 Å °0.0145 Å °0.0087 Å °0.0117 Å °-0.0029 Å °0.0267 Å °-0.0168 Å °0.0545 Å °0.0152 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 270
2X-RAY DIFFRACTION1B1 - 7

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