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- PDB-5y28: Crystal structure of H. pylori HtrA with PDZ2 deletion -

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Basic information

Entry
Database: PDB / ID: 5y28
TitleCrystal structure of H. pylori HtrA with PDZ2 deletion
Components
  • Periplasmic serine endoprotease DegP-like
  • UNK-UNK-UNK-UNK
KeywordsHYDROLASE / Serine protease
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S1C, Do / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Thrombin, subunit H ...Peptidase S1C, Do / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Secreted serine protease HtrA
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.08606824134 Å
AuthorsZhang, Z. / Huang, Q. / Tao, X.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The unique trimeric assembly of the virulence factor HtrA fromHelicobacter pylorioccurs via N-terminal domain swapping.
Authors: Zhang, Z. / Huang, Q. / Tao, X. / Song, G. / Zheng, P. / Li, H. / Sun, H. / Xia, W.
History
DepositionJul 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Mar 27, 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: Periplasmic serine endoprotease DegP-like
B: Periplasmic serine endoprotease DegP-like
C: Periplasmic serine endoprotease DegP-like
G: UNK-UNK-UNK-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2865
Polymers115,2244
Non-polymers621
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-48 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.910, 91.500, 120.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Periplasmic serine endoprotease DegP-like


Mass: 38307.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: hp1018/19 / Plasmid: PET-47b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: G2J5T2, peptidase Do
#2: Protein/peptide UNK-UNK-UNK-UNK


Mass: 302.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: hp1018/19 / Plasmid: PET-47b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M proline, 18%-20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 18846 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 87.4329479435 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Rrim(I) all: 0.104 / Χ2: 0.914 / Net I/σ(I): 7.2 / Num. measured all: 151679
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-33.61.3450.550.8071.570.80994
3-3.123.60.7170.7590.430.8370.81994.7
3.12-3.273.60.4910.8330.2950.5740.85496.6
3.27-3.443.60.3050.9180.1840.3560.9197.6
3.44-3.653.60.2170.9560.1310.2550.95398.8
3.65-3.943.70.1550.9760.0940.1821.01798.8
3.94-4.333.70.0960.9890.0590.1131.09799
4.33-4.963.60.0670.9920.0420.081.04498.9
4.96-6.243.60.0580.9940.0360.0680.86799
6.24-503.70.0450.9950.0280.0530.76198.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 3.08606824134→43.876174982 Å / SU ML: 0.467911550228 / Cross valid method: FREE R-VALUE / σ(F): 1.33504940564 / Phase error: 33.433123921
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.298384035637 959 5.11439389899 %
Rwork0.257333880111 17792 -
obs0.259468200327 18751 99.5487364621 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.3940086915 Å2
Refinement stepCycle: LAST / Resolution: 3.08606824134→43.876174982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 4 5 5193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002323722769485229
X-RAY DIFFRACTIONf_angle_d0.5382044177147100
X-RAY DIFFRACTIONf_chiral_restr0.0470381097668892
X-RAY DIFFRACTIONf_plane_restr0.00423623452234920
X-RAY DIFFRACTIONf_dihedral_angle_d14.63444870863125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0861-3.24870.3630583854091300.3149965723272503X-RAY DIFFRACTION99.8861911988
3.2487-3.45220.341992670271250.2813781075712525X-RAY DIFFRACTION99.8869204674
3.4522-3.71860.3631220723241420.2678645286672486X-RAY DIFFRACTION99.6965098634
3.7186-4.09260.2910322562861380.2672598653512524X-RAY DIFFRACTION99.4396712738
4.0926-4.68420.3042868008681380.229922805492520X-RAY DIFFRACTION99.1791044776
4.6842-5.89930.2783568838541340.25402767852561X-RAY DIFFRACTION99.5199409158
5.8993-43.88060.2750251504191520.2528364906722673X-RAY DIFFRACTION99.2970123023

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