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- PDB-5f5k: E.Coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMP... -

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Basic information

Entry
Database: PDB / ID: 5f5k
TitleE.Coli GlpG Y205F mutant complexed with aldehyde inhibitor in DMPC/CHAPSO bicelle
Components
  • Peptidic derivative of Gurken: ACE-ARG-LYS-VAL-ARG-MET-ALA-aldehyde
  • Rhomboid protease GlpG
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GlpG / Rhomboid / intramembrane protease / bicelle / aldehyde inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


maternal determination of dorsal/ventral axis, ovarian follicular epithelium, germ-line encoded / dorsal/ventral axis specification, ovarian follicular epithelium / anterior/posterior axis specification, follicular epithelium / determination of dorsal identity / chorion-containing eggshell pattern formation / oocyte anterior/posterior axis specification / oocyte microtubule cytoskeleton organization / oocyte dorsal/ventral axis specification / imaginal disc-derived wing vein specification / dorsal appendage formation ...maternal determination of dorsal/ventral axis, ovarian follicular epithelium, germ-line encoded / dorsal/ventral axis specification, ovarian follicular epithelium / anterior/posterior axis specification, follicular epithelium / determination of dorsal identity / chorion-containing eggshell pattern formation / oocyte anterior/posterior axis specification / oocyte microtubule cytoskeleton organization / oocyte dorsal/ventral axis specification / imaginal disc-derived wing vein specification / dorsal appendage formation / positive regulation of border follicle cell migration / rhomboid protease / anterior/posterior pattern specification / epidermal growth factor receptor binding / epidermal growth factor receptor signaling pathway / endopeptidase activity / cell surface receptor signaling pathway / receptor ligand activity / serine-type endopeptidase activity / proteolysis / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Protein Gurken/Spitz / 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 family / Rhomboid-like superfamily ...Protein Gurken/Spitz / 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 family / Rhomboid-like superfamily / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rhomboid protease GlpG / Rhomboid protease GlpG / Protein gurken
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 2.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_poly / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,5732
Polymers24,5732
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-6 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.320, 96.120, 62.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

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Components

#1: Protein Rhomboid protease GlpG / Intramembrane serine protease


Mass: 23800.133 Da / Num. of mol.: 1 / Fragment: UNP residues 87-276 / Mutation: Y205F
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-ARG-LYS-VAL-ARG-MET-ALA-aldehyde


Mass: 773.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P42287*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.5M NaCl, 0.1M Sodium Acetate pH 5, 5% Glycerol, 7% DMPC/CHAPSO bicelle

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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: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.3→50.01 Å / Num. obs: 9474 / % possible obs: 97.6 % / Redundancy: 5.1 % / Net I/σ(I): 5.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.873 / SU B: 15.711 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R: 0.506 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28807 401 4.8 %RANDOM
Rwork0.23439 ---
obs0.23707 7947 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.172 Å2
Baniso -1Baniso -2Baniso -3
1-5.46 Å20 Å20 Å2
2---0.74 Å20 Å2
3----4.72 Å2
Refinement stepCycle: 1 / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 0 50 1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191495
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9222031
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7555180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04722.10557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68115234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.148156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211107
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_it3.3524.792728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.5177.148904
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8765.144767
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.53145.2346491
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 27 -
Rwork0.362 557 -
obs--97.5 %

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