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- PDB-7xs2: Monomer structure of HtrA from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 7xs2
TitleMonomer structure of HtrA from Helicobacter pylori
ComponentsPeriplasmic serine endoprotease DegP-like
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 / Peptidase S1, PA clan
Similarity search - Domain/homology
Serine protease (HtrA)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCui, L. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Crystal structures and solution conformations of HtrA from Helicobacter pylori reveal pH-dependent oligomeric conversion and conformational rearrangements.
Authors: Cui, L. / Shi, X. / Li, H. / Wang, S. / Guo, L. / Lan, Z. / Dai, Y. / Zhang, Q. / Wu, Y. / Liu, W.
History
DepositionMay 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic serine endoprotease DegP-like


Theoretical massNumber of molelcules
Total (without water)47,8541
Polymers47,8541
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17880 Å2
Unit cell
Length a, b, c (Å)146.199, 146.199, 94.231
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Periplasmic serine endoprotease DegP-like


Mass: 47854.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_1019 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25663, peptidase Do
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 0.1 M sodium citrate, pH 3.4, 2.7 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.15→75.59 Å / Num. obs: 32753 / % possible obs: 100 % / Redundancy: 35.7 % / CC1/2: 0.999 / Net I/σ(I): 23.8
Reflection shellResolution: 2.15→2.27 Å / Num. unique obs: 4671 / Rpim(I) all: 0.421

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PV2

3pv2


Resolution: 2.15→63.306 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1662 5.08 %
Rwork0.2429 31081 -
obs0.2443 32743 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.02 Å2 / Biso mean: 79.3825 Å2 / Biso min: 30.6 Å2
Refinement stepCycle: final / Resolution: 2.15→63.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 0 72 2923
Biso mean---61.38 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082875
X-RAY DIFFRACTIONf_angle_d1.1293877
X-RAY DIFFRACTIONf_chiral_restr0.065467
X-RAY DIFFRACTIONf_plane_restr0.005502
X-RAY DIFFRACTIONf_dihedral_angle_d4.481758
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.15-2.21330.40191570.3472499
2.2133-2.28470.38211150.32922567
2.2847-2.36640.37891490.32562532
2.3664-2.46110.31091430.30012531
2.4611-2.57310.33731400.29282547
2.5731-2.70880.39961350.29242575
2.7088-2.87850.31311230.29742582
2.8785-3.10080.30861500.28422562
3.1008-3.41280.32731260.25712614
3.4128-3.90660.27881410.23812607
3.9066-4.92160.21231380.19152651
4.9216-63.3060.21831450.22162814
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.631-0.83840.90774.9712-0.05762.98430.03870.6652-0.08310.2166-0.04430.6557-0.1784-0.0569-0.01560.3233-0.04040.01860.4599-0.08830.3849110.05949.62210.656
21.35120.60190.98280.45420.39562.3950.20231.5649-1.02980.10080.3162-0.21770.92221.2001-0.15840.68630.2283-0.1661.2636-0.52790.8962124.57639.697.427
35.29121.50870.51337.3049-1.12025.22620.1804-0.7514-0.06290.1841-0.77290.37580.3562-0.01260.46470.5938-0.2146-0.03180.5584-0.14860.4033129.99825.4752.801
46.1792.92610.3745.25150.6475.0196-0.8430.2868-0.2609-0.83540.6326-0.5268-1.57340.72540.27110.811-0.30290.02240.6822-0.15010.4226102.78716.845-2.129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 46:207 )A46 - 207
2X-RAY DIFFRACTION2( CHAIN A AND RESID 208:337 )A208 - 337
3X-RAY DIFFRACTION3( CHAIN A AND RESID 338:373 )A338 - 373
4X-RAY DIFFRACTION4( CHAIN A AND RESID 374:433 )A374 - 433

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