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- PDB-7qo8: Structure of Protease1 from Pyrococcus horikoshii in space group ... -

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Basic information

Entry
Database: PDB / ID: 7qo8
TitleStructure of Protease1 from Pyrococcus horikoshii in space group 19 with a hexamer in the asymmetric unit
ComponentsDeglycase PH1704
KeywordsHYDROLASE / protease 1 / hexamer
Function / homology
Function and homology information


protein deglycase / protein deglycase activity / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / cytoplasm
Similarity search - Function
Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEngilberge, S. / Gabel, F. / Girard, E.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Medical contrast agents as promising tools for biomacromolecular SAXS experiments.
Authors: Gabel, F. / Engilberge, S. / Schmitt, E. / Thureau, A. / Mechulam, Y. / Perez, J. / Girard, E.
History
DepositionDec 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deglycase PH1704
B: Deglycase PH1704
C: Deglycase PH1704
D: Deglycase PH1704
E: Deglycase PH1704
F: Deglycase PH1704
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,67114
Polymers111,9036
Non-polymers7698
Water18,1951010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-73 kcal/mol
Surface area35200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.741, 123.636, 129.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLU(chain 'A' and (resid 1 through 36 or resid 38...AA1 - 361 - 36
12GLYGLYILEILE(chain 'A' and (resid 1 through 36 or resid 38...AA38 - 8538 - 85
13LYSLYSLEULEU(chain 'A' and (resid 1 through 36 or resid 38...AA88 - 11288 - 112
14GLYGLYLYSLYS(chain 'A' and (resid 1 through 36 or resid 38...AA114 - 166114 - 166
25METMETGLUGLU(chain 'B' and (resid 1 through 36 or resid 38...BB1 - 361 - 36
26GLYGLYILEILE(chain 'B' and (resid 1 through 36 or resid 38...BB38 - 8538 - 85
27LYSLYSLEULEU(chain 'B' and (resid 1 through 36 or resid 38...BB88 - 11288 - 112
28GLYGLYLYSLYS(chain 'B' and (resid 1 through 36 or resid 38...BB114 - 166114 - 166
39METMETGLUGLU(chain 'C' and (resid 1 through 36 or resid 38...CC1 - 361 - 36
310GLYGLYILEILE(chain 'C' and (resid 1 through 36 or resid 38...CC38 - 8538 - 85
311LYSLYSLEULEU(chain 'C' and (resid 1 through 36 or resid 38...CC88 - 11288 - 112
312GLYGLYLYSLYS(chain 'C' and (resid 1 through 36 or resid 38...CC114 - 166114 - 166
413METMETGLUGLU(chain 'D' and (resid 1 through 36 or resid 38...DD1 - 361 - 36
414GLYGLYILEILE(chain 'D' and (resid 1 through 36 or resid 38...DD38 - 8538 - 85
415LYSLYSLEULEU(chain 'D' and (resid 1 through 36 or resid 38...DD88 - 11288 - 112
416GLYGLYLYSLYS(chain 'D' and (resid 1 through 36 or resid 38...DD114 - 166114 - 166
517METMETGLUGLU(chain 'E' and (resid 1 through 36 or resid 38...EE1 - 361 - 36
518GLYGLYILEILE(chain 'E' and (resid 1 through 36 or resid 38...EE38 - 8538 - 85
519LYSLYSLEULEU(chain 'E' and (resid 1 through 36 or resid 38...EE88 - 11288 - 112
520GLYGLYLYSLYS(chain 'E' and (resid 1 through 36 or resid 38...EE114 - 166114 - 166
621METMETGLUGLU(chain 'F' and (resid 1 through 36 or resid 38...FF1 - 361 - 36
622GLYGLYILEILE(chain 'F' and (resid 1 through 36 or resid 38...FF38 - 8538 - 85
623LYSLYSLEULEU(chain 'F' and (resid 1 through 36 or resid 38...FF88 - 11288 - 112
624GLYGLYLYSLYS(chain 'F' and (resid 1 through 36 or resid 38...FF114 - 166114 - 166

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Components

#1: Protein
Deglycase PH1704 / Intracellular protease PH1704 / Protease 1


Mass: 18650.418 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1704 / Production host: Escherichia coli (E. coli)
References: UniProt: O59413, protein deglycase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1010 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.13 Å3/Da / Density % sol: 70.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM tri-sodium citrate pH 5.6, 200 mM sodium potassium tartrate, 1.9 to 2.4 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.95→70.72 Å / Num. obs: 135285 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.75 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.068 / Net I/σ(I): 11.8
Reflection shellResolution: 1.95→2.05 Å / Num. unique obs: 19324 / CC1/2: 0.567 / Rpim(I) all: 0.673

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q3T

6q3t


Resolution: 1.95→18.59 Å / SU ML: 0.1983 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.204 2000 1.48 %
Rwork0.1815 132946 -
obs0.1818 134946 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→18.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7836 0 40 1010 8886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00958084
X-RAY DIFFRACTIONf_angle_d1.102510947
X-RAY DIFFRACTIONf_chiral_restr0.06891192
X-RAY DIFFRACTIONf_plane_restr0.00671399
X-RAY DIFFRACTIONf_dihedral_angle_d16.78032987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.34321360.30969088X-RAY DIFFRACTION96.85
2-2.050.26251440.27049414X-RAY DIFFRACTION99.97
2.05-2.110.27681370.25939449X-RAY DIFFRACTION99.96
2.11-2.180.29481380.24299435X-RAY DIFFRACTION100
2.18-2.260.25831520.22339452X-RAY DIFFRACTION99.99
2.26-2.350.25111350.21249461X-RAY DIFFRACTION100
2.35-2.450.24771500.20259476X-RAY DIFFRACTION100
2.45-2.580.21061350.19979458X-RAY DIFFRACTION100
2.58-2.740.22521480.18749503X-RAY DIFFRACTION99.98
2.74-2.960.17861390.18139510X-RAY DIFFRACTION99.99
2.96-3.250.19831440.17099559X-RAY DIFFRACTION100
3.25-3.720.17351480.159565X-RAY DIFFRACTION100
3.72-4.670.15041470.13369640X-RAY DIFFRACTION99.98
4.67-18.590.17841470.15969936X-RAY DIFFRACTION99.88

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