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- PDB-6xrp: Crystal structure of GlpG in complex with peptide ketoamide inhib... -

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Basic information

Entry
Database: PDB / ID: 6xrp
TitleCrystal structure of GlpG in complex with peptide ketoamide inhibitor, Ac-RVWHA-ketoamide-phenylbutyl
Components
  • Rhomboid protease GlpG
  • peptide ketoamide inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GlpG / rhomboid protease / HYDROLASE-HYDROLASE INHIBITOR complex / membrane protein
Function / homology
Function and homology information


rhomboid protease / 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
N-(4-phenylbutyl)formamide / Rhomboid protease GlpG / Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionJul 13, 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 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhomboid protease GlpG
B: peptide ketoamide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7343
Polymers24,5572
Non-polymers1771
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-9 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.460, 109.460, 129.471
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Rhomboid protease GlpG / Intramembrane serine protease


Mass: 23816.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG, SK83_00858 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0J2E248, UniProt: P09391*PLUS, rhomboid protease
#2: Protein/peptide peptide ketoamide inhibitor


Mass: 740.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-V87 / N-(4-phenylbutyl)formamide


Mass: 177.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
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: 0.9712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9712 Å / Relative weight: 1
ReflectionResolution: 2.3→57.43 Å / Num. obs: 23475 / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1315 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2148refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IC8

2ic8


Resolution: 2.4→54.73 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 36.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 1116 4.94 %
Rwork0.2327 21461 -
obs0.2332 22577 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.42 Å2 / Biso mean: 70 Å2 / Biso min: 43.6 Å2
Refinement stepCycle: final / Resolution: 2.4→54.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 13 22 1522
Biso mean--86.61 69.93 -
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011553
X-RAY DIFFRACTIONf_angle_d1.0392106
X-RAY DIFFRACTIONf_chiral_restr0.054223
X-RAY DIFFRACTIONf_plane_restr0.005252
X-RAY DIFFRACTIONf_dihedral_angle_d16.867846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.50930.52541370.41182669100
2.5093-2.64160.36371300.34822705100
2.6416-2.8070.39041320.30362713100
2.807-3.02380.33351380.2842678100
3.0238-3.3280.31291260.23812734100
3.328-3.80950.24551270.2287265199
3.8095-4.79910.19541600.1889264999

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