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- PDB-5f5d: Crystal structures and Inhibition kinetics reveal a two-state cat... -

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Basic information

Entry
Database: PDB / ID: 5f5d
TitleCrystal structures and Inhibition kinetics reveal a two-state catalytic mechanism with drug design implications for rhomboid proteolysis
ComponentsRhomboid protease GlpG
KeywordsHYDROLASE / Intramembrane protease / rhomboid / Bicelle
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 24, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid protease GlpG


Theoretical massNumber of molelcules
Total (without water)23,8001
Polymers23,8001
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.185, 98.147, 62.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.5M NaCl, 5% Glycerol, 0.1M Sodium acetate pH5, 7% DMPC/CHAPSO bicelle

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.981 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 10370 / % possible obs: 98.4 % / Redundancy: 6.8 % / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.9 / % possible all: 74.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IC8

2ic8


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.857 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.338
RfactorNum. reflection% reflectionSelection details
Rfree0.28384 384 5.2 %RANDOM
Rwork0.2079 ---
obs0.21189 6937 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.461 Å2
Baniso -1Baniso -2Baniso -3
1-6.56 Å20 Å2-0 Å2
2---2.03 Å20 Å2
3----4.53 Å2
Refinement stepCycle: 1 / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 0 45 1442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.9241966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98222.10557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.55915224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.402156
X-RAY DIFFRACTIONr_chiral_restr0.1320.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211079
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_it5.0135.487694
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.2318.184864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.5876.013750
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.99251.9956106
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 30 -
Rwork0.228 542 -
obs--99.48 %

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