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- PDB-6vj8: Crystal structure of GlpG in complex with peptide chloromethylket... -

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Basic information

Entry
Database: PDB / ID: 6vj8
TitleCrystal structure of GlpG in complex with peptide chloromethylketone inhibitor
Components
  • Peptide chloromethylketone inhibitor
  • Rhomboid family intramembrane serine protease GlpG
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / complex / GlpG / rhomboid protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


rhomboid protease / membrane => GO:0016020 / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
ACE-VAL-ARG-MET-QZA / Rhomboid family intramembrane serine protease GlpG / Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUrban, S. / Cho, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01AI066025 United States
CitationJournal: Cell Chem Biol / Year: 2020
Title: Designed Parasite-Selective Rhomboid Inhibitors Block Invasion and Clear Blood-Stage Malaria.
Authors: Gandhi, S. / Baker, R.P. / Cho, S. / Stanchev, S. / Strisovsky, K. / Urban, S.
History
DepositionJan 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: 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 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid family intramembrane serine protease GlpG
B: Peptide chloromethylketone inhibitor


Theoretical massNumber of molelcules
Total (without water)22,4642
Polymers22,4642
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area9280 Å2
Unit cell
Length a, b, c (Å)110.049, 110.049, 127.311
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 family intramembrane serine protease GlpG


Mass: 21927.043 Da / Num. of mol.: 1 / Fragment: UNP residue 61-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG, EVY14_07190 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C43(DE3) / References: UniProt: A0A4Q6HQV3, UniProt: P09391*PLUS
#2: Protein/peptide Peptide chloromethylketone inhibitor


Type: Oligopeptide / Class: Inhibitor / Mass: 537.139 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: peptide derivative in which the N-terminus is acetylated and C-terminus ALA is modified to chloromethylketone
Source: (synth.) Drosophila melanogaster (fruit fly) / References: ACE-VAL-ARG-MET-QZA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris, pH 8.5, 3 M sodium nitrate, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.3→76.33 Å / Num. obs: 13264 / % possible obs: 99.1 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.568 / Num. unique obs: 1293

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IC8

2ic8


Resolution: 2.3→50.01 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.905 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.203
RfactorNum. reflection% reflectionSelection details
Rfree0.25225 648 4.9 %RANDOM
Rwork0.21808 ---
obs0.21983 12584 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.113 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å2-1.01 Å20 Å2
2---2.03 Å20 Å2
3---6.57 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 0 20 1482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191509
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.391.9272050
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.515181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44722.06958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23215235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.817156
X-RAY DIFFRACTIONr_chiral_restr0.1540.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211124
X-RAY DIFFRACTIONr_gen_planes_other
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_it6.1685.575732
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.8178.33910
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.8346.157777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.5046385
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 41 -
Rwork0.314 919 -
obs--100 %

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