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- PDB-7xs0: Trimer structure of HtrA from Helicobacter pylori bound with a tr... -

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Basic information

Entry
Database: PDB / ID: 7xs0
TitleTrimer structure of HtrA from Helicobacter pylori bound with a tripeptide
Components
  • Periplasmic serine endoprotease DegP-like
  • UNK-UNK-UNK
KeywordsHYDROLASE / serine protease
Function / homology
Function and homology information


peptidase Do / periplasmic space / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase M50 / Peptidase family M50 / 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
Periplasmic serine endoprotease DegP-like
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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

Downloads & links

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Assembly

Deposited unit
A: Periplasmic serine endoprotease DegP-like
B: UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)48,1272
Polymers48,1272
Non-polymers00
Water1,17165
1
A: Periplasmic serine endoprotease DegP-like
B: UNK-UNK-UNK

A: Periplasmic serine endoprotease DegP-like
B: UNK-UNK-UNK

A: Periplasmic serine endoprotease DegP-like
B: UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)144,3826
Polymers144,3826
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)139.506, 139.506, 191.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

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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 26695 (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_1019 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25663, peptidase Do
#2: Protein/peptide UNK-UNK-UNK


Mass: 273.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris, pH 6.5, 2.2 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 22542 / % possible obs: 100 % / Redundancy: 17.7 % / Biso Wilson estimate: 37.69 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.016 / Rrim(I) all: 0.066 / Χ2: 0.975 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6618.41.63414600.8480.3831.6790.991100
2.66-2.7318.41.19915000.9150.281.2321.01100
2.73-2.818.40.91514860.9370.2140.940.994100
2.8-2.8818.10.62614600.9710.1480.6440.993100
2.88-2.9817.80.43715000.9860.1050.451.009100
2.98-3.0817.10.29214890.9910.0720.3011.057100
3.08-3.2116.60.19115110.9940.0480.1971.063100
3.21-3.3518.50.14314810.9970.0340.1471.07100
3.35-3.5318.30.09814880.9980.0230.11.086100
3.53-3.7518.10.07814990.9980.0190.081.028100
3.75-4.0417.20.06115150.9990.0150.0631.001100
4.04-4.4517.50.05114990.9980.0130.0520.96100
4.45-5.0918.20.04615320.9990.0110.0480.9199.9
5.09-6.4116.70.04415350.9990.0110.0450.764100
6.41-5016.80.0415870.9970.010.0410.682100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XS2

7xs2


Resolution: 2.59→41.21 Å / SU ML: 0.3058 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.7718
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 1125 5.12 %
Rwork0.2308 20845 -
obs0.2322 21970 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.9 Å2
Refinement stepCycle: LAST / Resolution: 2.59→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 0 65 2939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462901
X-RAY DIFFRACTIONf_angle_d0.88433909
X-RAY DIFFRACTIONf_chiral_restr0.0539467
X-RAY DIFFRACTIONf_plane_restr0.0074505
X-RAY DIFFRACTIONf_dihedral_angle_d7.6229392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.70.32061130.27432089X-RAY DIFFRACTION78.61
2.7-2.850.29521350.26512610X-RAY DIFFRACTION98.46
2.85-3.020.23351350.23952675X-RAY DIFFRACTION100
3.02-3.260.2951460.23772628X-RAY DIFFRACTION100
3.26-3.580.23191470.21872681X-RAY DIFFRACTION100
3.59-4.10.22661450.22012683X-RAY DIFFRACTION99.89
4.1-5.170.24611450.20262709X-RAY DIFFRACTION99.96
5.17-41.210.27861590.2492770X-RAY DIFFRACTION99.73
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)
12.934053920740.562211904852-0.2849996600372.98627013837-0.03077254397611.662930730710.131666502338-0.0258866745050.66968290661-0.147169415318-0.1037001111260.607273196056-0.34729887926-0.0917802337947-0.01842738966150.1908197858310.0271586085039-0.03859766017010.199761459291-0.03316369438450.36351923574-16.30994626779.87774689931-35.707520428
22.251339158590.727831723609-0.5674416130031.424859719490.447787575461.36486926189-0.0131082717635-0.869055352150.7572902622940.550855973840.07229002283310.1060446768280.2578983496590.06863943925890.01616082803370.1727219737310.0434691445778-0.09967468265670.56848043347-0.1862889162170.394379482639-35.630898619-9.67191363168-22.4867118188
30.425534113522-0.2287799623230.08971072193430.2821626497820.5693954519330.9913157199540.12030586838-0.592744614592-0.0417316317577-0.1530687089660.399657935164-0.574079074191-0.6374691443661.295920746140.1016303918560.897505303791-0.6098447044930.2533733262092.16969132567-0.505006687120.311121763859-29.54942457859.82469952561-6.22592992088
40.1621764416650.2856389528690.2083968222740.6804687536640.2233921941490.384097780742-0.268831601871-0.6131486773920.3642173428560.790634156049-0.0194252357428-0.693903057233-0.1497113523780.6965462267930.2385086550450.41727419201-0.00406299615458-0.08927748052741.11850023265-0.227128691580.496420710845-33.4229439651-6.6777976249-16.8511174555
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -5 through 250 )AA-5 - 2501 - 174
22chain 'A' and (resid 251 through 351 )AA251 - 351175 - 271
33chain 'A' and (resid 352 through 474 )AA352 - 474272 - 376
44chain 'B' and (resid 1 through 3 )BB1 - 31 - 3

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