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- PDB-6vj9: Crystal structure of GlpG in complex with peptide boronate inhibitor -

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Basic information

Entry
Database: PDB / ID: 6vj9
TitleCrystal structure of GlpG in complex with peptide boronate inhibitor
Components
  • ACE-VAL-ARG-MET-B2A
  • 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 / endopeptidase activity / membrane => GO:0016020 / 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-B2A / 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 / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhomboid family intramembrane serine protease GlpG
B: ACE-VAL-ARG-MET-B2A


Theoretical massNumber of molelcules
Total (without water)22,4302
Polymers22,4302
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-7 kcal/mol
Surface area9180 Å2
Unit cell
Length a, b, c (Å)111.310, 111.310, 125.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

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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 ACE-VAL-ARG-MET-B2A


Type: Oligopeptide / Class: Inhibitor / Mass: 502.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: ACE-VAL-ARG-MET-B2A
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.33 Å3/Da / Density % sol: 63.04 %
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: 0.9718 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: 0.9718 Å / Relative weight: 1
ReflectionResolution: 2.3→32.13 Å / Num. obs: 13444 / % possible obs: 99.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.621 / Num. unique obs: 1296

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IC8

2ic8


Resolution: 2.3→32.15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.514 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.25839 683 5.1 %RANDOM
Rwork0.22732 ---
obs0.22894 12754 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å2-1.12 Å20 Å2
2---2.23 Å20 Å2
3---7.24 Å2
Refinement stepCycle: 1 / Resolution: 2.3→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 0 19 1477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.5992049
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.425181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08120.93864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54715233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.604156
X-RAY DIFFRACTIONr_chiral_restr0.1370.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021129
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_it5.3875.915730
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.6638.838908
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.6276.609776
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.4466429
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
Rfree0.393 41 -
Rwork0.397 934 -
obs--99.8 %

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