[English] 日本語
Yorodumi
- PDB-5y2d: Crystal structure of H. pylori HtrA -

+
Open data


ID or keywords:

Loading...

-
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


peptidase Do / metalloendopeptidase activity / 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 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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Periplasmic serine endoprotease DegP-like
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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"

-
Components

-
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

-
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)

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more