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- PDB-5mt7: Structure of E.coli GlpG in complex with peptide derived inhibito... -

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Basic information

Entry
Database: PDB / ID: 5mt7
TitleStructure of E.coli GlpG in complex with peptide derived inhibitor Ac-VRHA-cmk
Components
  • ACE-VAL-ARG-HIS-ALA-0QE
  • 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 domain / 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: 2.05 Å
AuthorsVinothkumar, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184322 United Kingdom
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 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid protease GlpG
B: ACE-VAL-ARG-HIS-ALA-0QE


Theoretical massNumber of molelcules
Total (without water)20,9992
Polymers20,9992
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.944, 110.944, 126.343
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: 20457.234 Da / Num. of mol.: 1 / Fragment: UNP Residues 91-271
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-VAL-ARG-HIS-ALA-0QE


Mass: 542.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 63.47 %
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: 2.05→44.9 Å / Num. obs: 18936 / % possible obs: 99.7 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 28
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.795 / % possible all: 96.5

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Processing

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

2xov


Resolution: 2.05→44.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.695 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22479 908 4.8 %RANDOM
Rwork0.20184 ---
obs0.20283 18022 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.712 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å2-0.86 Å2-0 Å2
2---1.72 Å2-0 Å2
3---5.58 Å2
Refinement stepCycle: 1 / Resolution: 2.05→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 1 18 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191519
X-RAY DIFFRACTIONr_bond_other_d0.0020.021439
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9282065
X-RAY DIFFRACTIONr_angle_other_deg0.93733284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1375182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.96721.55258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57215233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.422157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
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_it1.8374.172736
X-RAY DIFFRACTIONr_mcbond_other1.8354.17735
X-RAY DIFFRACTIONr_mcangle_it2.7136.238916
X-RAY DIFFRACTIONr_mcangle_other2.7136.239917
X-RAY DIFFRACTIONr_scbond_it2.5654.593783
X-RAY DIFFRACTIONr_scbond_other2.5654.593783
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1076.7611151
X-RAY DIFFRACTIONr_long_range_B_refined5.84949.4111847
X-RAY DIFFRACTIONr_long_range_B_other5.84449.4141847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 61 -
Rwork0.307 1274 -
obs--96.32 %
Refinement TLS params.Method: refined / Origin x: 15.3825 Å / Origin y: 11.6422 Å / Origin z: 145.2105 Å
111213212223313233
T0.1543 Å2-0.051 Å2-0.0855 Å2-0.1192 Å2-0.0106 Å2--0.082 Å2
L1.5069 °20.7576 °2-0.8602 °2-1.4166 °2-0.2546 °2--2.1965 °2
S-0.0256 Å °-0.1023 Å °0.0526 Å °-0.0397 Å °0.0591 Å °-0.0012 Å °0.2636 Å °0.0336 Å °-0.0335 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 270
2X-RAY DIFFRACTION1B1 - 6

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