[English] 日本語
Yorodumi
- PDB-6ew9: CRYSTAL STRUCTURE OF DEGS STRESS SENSOR PROTEASE IN COMPLEX WITH ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ew9
TitleCRYSTAL STRUCTURE OF DEGS STRESS SENSOR PROTEASE IN COMPLEX WITH ACTIVATING DNRLGLVYQF PEPTIDE
Components
  • DNRLGLVYQF PEPTIDE
  • Serine endoprotease DegS
KeywordsHYDROLASE / PROTEASE / STRESS-SENSOR / PDZ / PERIPLASM / SERINE PROTEIASE / ACTIVATOR PEPTIDE
Function / homology
Function and homology information


peptidase Do / cellular response to misfolded protein / serine-type peptidase activity / outer membrane-bounded periplasmic space / peptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin ...Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVetter, I.R. / Porfetye, A.T. / Stege, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCRC1093 Germany
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Identification of Noncatalytic Lysine Residues from Allosteric Circuits via Covalent Probes.
Authors: Bongard, J. / Lorenz, M. / Vetter, I.R. / Stege, P. / Porfetye, A.T. / Schmitz, A.L. / Kaschani, F. / Wolf, A. / Koch, U. / Nussbaumer, P. / Klebl, B. / Kaiser, M. / Ehrmann, M.
History
DepositionNov 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 7, 2018Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine endoprotease DegS
B: Serine endoprotease DegS
C: Serine endoprotease DegS
P: DNRLGLVYQF PEPTIDE
Q: DNRLGLVYQF PEPTIDE
R: DNRLGLVYQF PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,90315
Polymers103,4766
Non-polymers4279
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-127 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.600, 53.650, 132.500
Angle α, β, γ (deg.)90.000, 101.800, 90.000
Int Tables number3
Space group name H-MP121

-
Components

#1: Protein Serine endoprotease DegS / Site-1 protease DegS / S1P protease DegS / Site-1-type intramembrane protease


Mass: 33266.633 Da / Num. of mol.: 3 / Fragment: PROTEASE AND PDZ DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: degS, hhoB, htrH, b3235, JW3204 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon +RIL / References: UniProt: P0AEE3, peptidase Do
#2: Protein/peptide DNRLGLVYQF PEPTIDE


Mass: 1225.374 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 14.4% PEG 8000, 160 mM CaAc, 80 mM Na-cacodylate pH 6.5, 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→129.699 Å / Num. obs: 50358 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.72 % / Biso Wilson estimate: 45.998 Å2 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.175 / Net I/σ(I): 8.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2.2-2.266.591.4930.9436801.6299.6
2.26-2.321.3011.1136251.41799.8
2.32-2.391.1631.3135061.25699.9
2.39-2.461.0021.634051.08199.9
2.46-2.540.8241.9533230.8999.8
2.54-2.630.672.432030.72499.8
2.63-2.730.5552.8330610.60299.8
2.73-2.840.4563.4629770.49899.9
2.84-2.970.344.9328650.36799.8
2.97-3.110.2626.627320.28399.5
3.11-3.280.2098.225740.22699.9
3.28-3.480.1510.7924840.16299.8
3.48-3.720.11813.0523130.12999.7
3.72-4.020.09716.9921630.10599.5
4.02-4.40.07222.6619900.07899.4
4.4-4.920.06324.8518300.06999.7
4.92-5.680.07321.2115850.0899.5
5.68-6.960.07123.0713610.07799.1
6.96-9.840.04830.2810690.05299.1
9.840.03338.666120.03797.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.382 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.52
RfactorNum. reflection% reflection
Rfree0.2731 2518 5.01 %
Rwork0.2256 --
obs0.228 50307 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 52.6065 Å2 / Biso min: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6819 0 15 80 6914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.24250.39931390.351126442783100
2.2425-2.28820.36571360.335526152751100
2.2882-2.3380.36051380.313226352773100
2.338-2.39240.39431380.309926332771100
2.3924-2.45220.33981410.296426442785100
2.4522-2.51850.34981380.284126052743100
2.5185-2.59260.31721390.266126522791100
2.5926-2.67630.3761390.270526712810100
2.6763-2.77190.31551370.255226132750100
2.7719-2.88280.29091420.247426692811100
2.8828-3.0140.27621400.24226372777100
3.014-3.17290.28311420.238226542796100
3.1729-3.37160.30941380.234926502788100
3.3716-3.63180.26831400.219526762816100
3.6318-3.99710.26471400.206426562796100
3.9971-4.57490.21381410.173326732814100
4.5749-5.76180.21361410.188126922833100
5.7618-43.39020.23311490.19692770291999

+
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