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- PDB-6pja: Time-resolved structural snapshot of proteolysis by GlpG inside t... -

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Basic information

Entry
Database: PDB / ID: 6pja
TitleTime-resolved structural snapshot of proteolysis by GlpG inside the membrane
Components
  • Peptide aldehyde inhibitor
  • Rhomboid protease GlpG
KeywordsMEMBRANE PROTEIN / inhibitor
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: 2.6 Å
AuthorsUrban, S. / Cho, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI066025 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release.
Authors: Cho, S. / Baker, R.P. / Ji, M. / Urban, S.
History
DepositionJun 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 aldehyde inhibitor


Theoretical massNumber of molelcules
Total (without water)24,3482
Polymers24,3482
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-8 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.770, 99.490, 63.060
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG, APT88_21985, SK83_00858 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0J2E248, UniProt: P09391*PLUS, rhomboid protease
#2: Protein/peptide Peptide aldehyde inhibitor


Mass: 547.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Na-acetate pH 5.5, 3 M NaCl, and 5 % ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 2.5→58.52 Å / Num. obs: 7281 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rsym value: 0.065 / Net I/σ(I): 4.3
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.536 / Num. unique obs: 909

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→58.21 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.914 / SU B: 23.254 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R: 0.665 / ESU R Free: 0.309
RfactorNum. reflection% reflectionSelection details
Rfree0.26732 367 4.8 %RANDOM
Rwork0.26006 ---
obs0.26042 7281 94.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.459 Å2
Baniso -1Baniso -2Baniso -3
1-9.43 Å20 Å2-0 Å2
2---4.01 Å20 Å2
3----5.42 Å2
Refinement stepCycle: 1 / Resolution: 2.6→58.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 0 10 1453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121484
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.5922016
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09620.95263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74715232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.001156
X-RAY DIFFRACTIONr_chiral_restr0.1140.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021093
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_it4.5676.063721
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.9979.061896
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9436.206763
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.916107
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
Rfree0.384 20 -
Rwork0.439 554 -
obs--96.31 %

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