[English] 日本語
Yorodumi
- PDB-6jjl: Crystal structure of the DegP dodecamer with a modulator -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jjl
TitleCrystal structure of the DegP dodecamer with a modulator
Components
  • CYS-TYR-ARG-LYS-LEU
  • Periplasmic serine endoprotease DegP
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress ...peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress / periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, Do / 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 / Peptidase S1, PA clan
Similarity search - Domain/homology
Periplasmic serine endoprotease DegP
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsCho, H. / Choi, Y. / Lee, H.H. / Kim, S.
CitationJournal: Commun Biol / Year: 2020
Title: Over-activation of a nonessential bacterial protease DegP as an antibiotic strategy.
Authors: Cho, H. / Choi, Y. / Min, K. / Son, J.B. / Park, H. / Lee, H.H. / Kim, S.
History
DepositionFeb 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Periplasmic serine endoprotease DegP
B: Periplasmic serine endoprotease DegP
C: Periplasmic serine endoprotease DegP
D: Periplasmic serine endoprotease DegP
E: Periplasmic serine endoprotease DegP
F: Periplasmic serine endoprotease DegP
G: CYS-TYR-ARG-LYS-LEU
M: CYS-TYR-ARG-LYS-LEU
H: CYS-TYR-ARG-LYS-LEU
N: CYS-TYR-ARG-LYS-LEU
I: CYS-TYR-ARG-LYS-LEU
Q: CYS-TYR-ARG-LYS-LEU
J: CYS-TYR-ARG-LYS-LEU
O: CYS-TYR-ARG-LYS-LEU
K: CYS-TYR-ARG-LYS-LEU
R: CYS-TYR-ARG-LYS-LEU
L: CYS-TYR-ARG-LYS-LEU
P: CYS-TYR-ARG-LYS-LEU


Theoretical massNumber of molelcules
Total (without water)284,83118
Polymers284,83118
Non-polymers00
Water00
1
A: Periplasmic serine endoprotease DegP
B: Periplasmic serine endoprotease DegP
C: Periplasmic serine endoprotease DegP
D: Periplasmic serine endoprotease DegP
E: Periplasmic serine endoprotease DegP
F: Periplasmic serine endoprotease DegP
G: CYS-TYR-ARG-LYS-LEU
M: CYS-TYR-ARG-LYS-LEU
H: CYS-TYR-ARG-LYS-LEU
N: CYS-TYR-ARG-LYS-LEU
I: CYS-TYR-ARG-LYS-LEU
Q: CYS-TYR-ARG-LYS-LEU
J: CYS-TYR-ARG-LYS-LEU
O: CYS-TYR-ARG-LYS-LEU
K: CYS-TYR-ARG-LYS-LEU
R: CYS-TYR-ARG-LYS-LEU
L: CYS-TYR-ARG-LYS-LEU
P: CYS-TYR-ARG-LYS-LEU

A: Periplasmic serine endoprotease DegP
B: Periplasmic serine endoprotease DegP
C: Periplasmic serine endoprotease DegP
D: Periplasmic serine endoprotease DegP
E: Periplasmic serine endoprotease DegP
F: Periplasmic serine endoprotease DegP
G: CYS-TYR-ARG-LYS-LEU
M: CYS-TYR-ARG-LYS-LEU
H: CYS-TYR-ARG-LYS-LEU
N: CYS-TYR-ARG-LYS-LEU
I: CYS-TYR-ARG-LYS-LEU
Q: CYS-TYR-ARG-LYS-LEU
J: CYS-TYR-ARG-LYS-LEU
O: CYS-TYR-ARG-LYS-LEU
K: CYS-TYR-ARG-LYS-LEU
R: CYS-TYR-ARG-LYS-LEU
L: CYS-TYR-ARG-LYS-LEU
P: CYS-TYR-ARG-LYS-LEU


Theoretical massNumber of molelcules
Total (without water)569,66336
Polymers569,66336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)217.152, 123.519, 140.560
Angle α, β, γ (deg.)90.000, 118.000, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Periplasmic serine endoprotease DegP / Heat shock protein DegP / Protease Do


Mass: 46104.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: degP, htrA, ptd, b0161, JW0157 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0V0, peptidase Do
#2: Protein/peptide
CYS-TYR-ARG-LYS-LEU


Mass: 683.863 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 11% PEG3350, 0.1 M tacsimate pH 3.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 24531 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.045 / Rrim(I) all: 0.121 / Χ2: 1.944 / Net I/σ(I): 9.1 / Num. measured all: 176600
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.2-4.277.10.66512270.9210.2690.7181.776100
4.27-4.357.10.48412140.9530.1940.5221.908100
4.35-4.4370.4412070.920.180.4762.014100
4.43-4.527.20.4112290.9450.1640.4421.9100
4.52-4.627.20.39812210.9590.1590.4291.868100
4.62-4.737.20.36112040.9560.1450.391.77299.9
4.73-4.857.20.31312590.9760.1250.3371.742100
4.85-4.987.20.3112030.9730.1240.3341.725100
4.98-5.137.20.29212110.9820.1170.3151.662100
5.13-5.297.10.28412280.980.1140.3061.733100
5.29-5.4870.28212420.9780.1150.3041.691100
5.48-5.76.70.28312170.9690.1190.3081.771100
5.7-5.967.40.24812270.9870.0980.2671.771100
5.96-6.277.60.18412310.990.0720.1981.813100
6.27-6.667.60.14312270.9950.0560.1531.878100
6.66-7.187.50.10712280.9960.0420.1151.943100
7.18-7.97.50.08312340.9970.0330.0891.979100
7.9-9.037.50.05512430.9980.0210.0592.083100
9.03-11.367.30.04812490.9980.0190.0512.471100
11.36-506.40.05612300.9950.0240.0613.55396.9

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OTP

3otp


Resolution: 4.2→50 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.753 / SU B: 71.699 / SU ML: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.191
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3255 1262 5.1 %RANDOM
Rwork0.2477 ---
obs0.2516 23246 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 219.4 Å2 / Biso mean: 51.451 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20.06 Å2
2--0.83 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 4.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17212 0 0 0 17212
Num. residues----2370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01917346
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217535
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.97623401
X-RAY DIFFRACTIONr_angle_other_deg1.943340245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03652341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.43226.692656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.983153103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4271566
X-RAY DIFFRACTIONr_chiral_restr0.0430.22815
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023525
LS refinement shellResolution: 4.157→4.265 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 81 -
Rwork0.27 1470 -
all-1551 -
obs--84.48 %

+
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