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- PDB-8ab5: Structure of E. coli GlpG in complex with peptide derived inhibit... -

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Basic information

Entry
Database: PDB / ID: 8ab5
TitleStructure of E. coli GlpG in complex with peptide derived inhibitor Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]
Components
  • Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]
  • Rhomboid protease GlpG
KeywordsHYDROLASE / rhomboid / protease / GlpG / ketoamide / inhibitor
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
: / Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Providencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSkerlova, J. / Polovinkin, V. / Bach, K. / Borshchevskiy, V. / Strisovsky, K.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency.
Authors: Bach, K. / Dohnalek, J. / Skerlova, J. / Kuzmik, J. / Polachova, E. / Stanchev, S. / Majer, P. / Fanfrlik, J. / Pecina, A. / Rezac, J. / Lepsik, M. / Borshchevskiy, V. / Polovinkin, V. / Strisovsky, K.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 protease GlpG
B: Rhomboid protease GlpG
C: Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]
D: Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]


Theoretical massNumber of molelcules
Total (without water)42,3244
Polymers42,3244
Non-polymers00
Water39622
1
A: Rhomboid protease GlpG
C: Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]


Theoretical massNumber of molelcules
Total (without water)21,1622
Polymers21,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-6 kcal/mol
Surface area9350 Å2
MethodPISA
2
B: Rhomboid protease GlpG
D: Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]


Theoretical massNumber of molelcules
Total (without water)21,1622
Polymers21,1622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-7 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.540, 70.860, 66.000
Angle α, β, γ (deg.)90.000, 100.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rhomboid protease GlpG / Intramembrane serine protease


Mass: 20343.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glpG, b3424, JW5687 / Production host: Escherichia coli (E. coli) / References: UniProt: P09391, rhomboid protease
#2: Protein/peptide Ac-VRHA-conh-[4-(4-butyl)-phenoxy-1-phenyl-2-butyl]


Type: Peptide-like / Class: Inhibitor / Mass: 819.047 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria) / References: BIRD: PRD_002417
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 7.5 / Details: 2.65 M sodium malonate pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 2.4→29.5 Å / Num. obs: 16528 / % possible obs: 95.5 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.046 / Rrim(I) all: 0.105 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.493.61.103568315810.5150.6411.2821.388.5
8.98-29.544.80.03416293410.9980.0170.03835.196.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.7.2data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
XDSFeb 5, 2021 (BUILT 20210323)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mt6

5mt6


Resolution: 2.4→29.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.4826 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.483 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 868 5.3 %RANDOM
Rwork0.2175 ---
obs0.2203 15659 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.54 Å2 / Biso mean: 56.283 Å2 / Biso min: 35 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å22.21 Å2
2--0.11 Å20 Å2
3----2.43 Å2
Refinement stepCycle: final / Resolution: 2.4→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 58 22 2980
Biso mean--65.58 48.12 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133060
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172902
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.6274154
X-RAY DIFFRACTIONr_angle_other_deg2.2731.5936632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64720.781128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50415464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3141512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023352
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02760
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 51 -
Rwork0.31 1082 -
all-1133 -
obs--87.15 %

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