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- PDB-5f5b: Structure of E.Coli GlpG complexed with peptidic inhibitor Ac-VRMA-CHO -

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Basic information

Entry
Database: PDB / ID: 5f5b
TitleStructure of E.Coli GlpG complexed with peptidic inhibitor Ac-VRMA-CHO
Components
  • Rhomboid protease GlpG
  • peptidic derivative of Gurken: ACE-VAL-ARG-MET-ALA-aldehyde
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Rhomboid / membrane protease / aldehyde inhibitor / HYDROLASE-INHIBITOR complex / HYDROLASE-HYDROLASE INHIBITOR complex
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 / 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. / Dickey, S.W.
CitationJournal: Mol.Cell / Year: 2016
Title: Crystal Structures and Inhibition Kinetics Reveal a Two-Stage Catalytic Mechanism with Drug Design Implications for Rhomboid Proteolysis.
Authors: Cho, S. / Dickey, S.W. / Urban, S.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 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
Revision 2.0Jul 10, 2024Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid protease GlpG
B: peptidic derivative of Gurken: ACE-VAL-ARG-MET-ALA-aldehyde


Theoretical massNumber of molelcules
Total (without water)24,3032
Polymers24,3032
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-9 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.590, 110.590, 126.730
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: 23816.133 Da / Num. of mol.: 1 / Fragment: UNP residues 87-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG, SK83_00858 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (C43)
References: UniProt: A0A0J2E248, UniProt: P09391*PLUS, rhomboid protease
#2: Protein/peptide peptidic derivative of Gurken: ACE-VAL-ARG-MET-ALA-aldehyde


Mass: 486.652 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Aldehyde inhibitor of Rhomboid protease, modification at C-terminus by aldehyde group
Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4M NaNO3, 0.1M Tris pH7.5, 5% Glycerol, 0.2 % nonyl glucoside
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2→50.01 Å / Num. obs: 20167 / % possible obs: 99.3 % / Redundancy: 7.9 % / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IC8

2ic8


Resolution: 2.3→50.01 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.248 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 651 4.9 %RANDOM
Rwork0.213 ---
obs0.215 20167 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0.63 Å20 Å2
2---1.26 Å20 Å2
3---4.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 0 34 1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191533
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4781.9232083
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.065185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8892260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32915240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.752157
X-RAY DIFFRACTIONr_chiral_restr0.140.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211144
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_it5.7275.161745
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.2117.716928
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.2915.771788
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.4149.1126564
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
Rfree0.321 43 -
Rwork0.264 944 -
obs--100 %

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