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- PDB-5y2d: Crystal structure of H. pylori HtrA -

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Basic information

Entry
Database: PDB / ID: 5y2d
TitleCrystal structure of H. pylori HtrA
Components
  • (UNK-UNK-UNK-UNK-UNK-UNK-UNK- ...) x 2
  • Periplasmic serine endoprotease DegP-like
  • UNK-UNK-K-UNK-UNK-UNK-UNK-UNK-UNK-UNK
  • UNK-UNK-UNK
  • UNK-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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases ...: / Peptidase S1C, Do / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / 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)
Helicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.70009854828 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 25, 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: UNK-UNK-UNK
C: UNK-UNK-UNK-UNK-UNK
D: UNK-UNK-K-UNK-UNK-UNK-UNK-UNK-UNK-UNK
E: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
F: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)53,1496
Polymers53,1496
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area16440 Å2
Unit cell
Length a, b, c (Å)128.880, 128.880, 184.536
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Periplasmic serine endoprotease DegP-like


Mass: 50370.898 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 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: G2J5T2, peptidase Do

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Protein/peptide , 3 types, 3 molecules BCD

#2: Protein/peptide UNK-UNK-UNK


Mass: 231.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Production host: Escherichia coli (E. coli)
#3: Protein/peptide UNK-UNK-UNK-UNK-UNK


Mass: 373.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Production host: Escherichia coli (E. coli)
#4: Protein/peptide UNK-UNK-K-UNK-UNK-UNK-UNK-UNK-UNK-UNK


Mass: 786.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Production host: Escherichia coli (E. coli)

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UNK-UNK-UNK-UNK-UNK-UNK-UNK- ... , 2 types, 2 molecules EF

#5: Protein/peptide UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK


Mass: 586.638 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Production host: Escherichia coli (E. coli)
#6: Protein/peptide UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK


Mass: 799.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Production host: Escherichia coli (E. coli)

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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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.1 M DL-malic acid pH 7.0, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 6505 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 63.8079972517 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.037 / Rrim(I) all: 0.123 / Χ2: 1.04 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.72-3.8111.40.4884490.9440.1520.5111.055100
3.81-3.9111.30.3824460.9690.1190.41.069100
3.91-4.0311.20.2874700.9860.090.3011.049100
4.03-4.1611.30.2114370.9880.0650.2211.034100
4.16-4.3111.20.1854490.9940.0580.1941.061100
4.31-4.4811.20.1314460.9950.0410.1380.951100
4.48-4.6811.30.134530.9950.040.1360.966100
4.68-4.9311.20.1254580.9950.0390.1310.973100
4.93-5.2411.20.1224500.9960.0380.1281.027100
5.24-5.6411.10.1214620.9940.0380.1271.028100
5.64-6.21110.0854640.9970.0270.0890.961100
6.21-7.1110.0694600.9970.0220.0730.855100
7.1-8.9410.80.0544800.9950.0170.0560.884100
8.94-509.80.0494920.9980.0170.0521.85999.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHENIXphasing
RefinementResolution: 3.70009854828→44.4946700101 Å / SU ML: 0.468111806412 / Cross valid method: FREE R-VALUE / σ(F): 1.35739823429 / Phase error: 34.0435691982
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.334427242849 628 9.67791647403 %
Rwork0.331273373157 5861 -
obs0.331574575122 6489 99.8461301739 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.0221781202 Å2
Refinement stepCycle: LAST / Resolution: 3.70009854828→44.4946700101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 0 0 1853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01173719557031858
X-RAY DIFFRACTIONf_angle_d1.942827151472525
X-RAY DIFFRACTIONf_chiral_restr0.120142624119326
X-RAY DIFFRACTIONf_plane_restr0.0079644172896332
X-RAY DIFFRACTIONf_dihedral_angle_d20.8808413763563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-4.07220.2954379626721470.286846666411444X-RAY DIFFRACTION99.9371859296
4.0722-4.66090.3171899203281620.3009931103381439X-RAY DIFFRACTION100
4.6609-5.87020.3896440444721570.3795655743361466X-RAY DIFFRACTION100
5.8702-44.49790.3364767031031620.3481130047371512X-RAY DIFFRACTION99.4652406417

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