[English] 日本語
Yorodumi
- PDB-6ks5: Crystal structure of Legionella pneumophila deubiquitinase Ceg23 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ks5
TitleCrystal structure of Legionella pneumophila deubiquitinase Ceg23
ComponentsType IV secretion protein Dot
KeywordsHYDROLASE / enzyme
Function / homologymembrane => GO:0016020 / membrane / Type IV secretion protein Dot / Type IV secretion protein Dot
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsQiu, J.Z. / Ouyang, S.Y.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The bacterial deubiquitinase Ceg23 regulates the association of Lys-63-linked polyubiquitin molecules on theLegionellaphagosome.
Authors: Ma, K. / Zhen, X. / Zhou, B. / Gan, N. / Cao, Y. / Fan, C. / Ouyang, S. / Luo, Z.Q. / Qiu, J.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: 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: Type IV secretion protein Dot
B: Type IV secretion protein Dot


Theoretical massNumber of molelcules
Total (without water)81,5972
Polymers81,5972
Non-polymers00
Water00
1
A: Type IV secretion protein Dot


Theoretical massNumber of molelcules
Total (without water)40,7991
Polymers40,7991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type IV secretion protein Dot


Theoretical massNumber of molelcules
Total (without water)40,7991
Polymers40,7991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.350, 71.610, 142.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Type IV secretion protein Dot


Mass: 40798.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_07335 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S6F7D4, UniProt: Q5ZV21*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% polyethylene glycol 4000, 0.2 M sodium cacodylate (pH 6.0) and 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 2.8→64.02 Å / Num. obs: 17475 / % possible obs: 99 % / Redundancy: 12.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.036 / Rsym value: 0.128 / Net I/σ(I): 2
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 1226 / CC1/2: 0.901 / % possible all: 97

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.8→40.441 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.299 901 5.17 %
Rwork0.2735 16517 -
obs0.2748 17418 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.83 Å2 / Biso mean: 86.992 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.8→40.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4705 0 0 0 4705
Num. residues----614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.97540.34871440.3566266697
2.9754-3.2050.3351520.343268599
3.205-3.52740.37561600.3409271399
3.5274-4.03740.32171370.2893275599
4.0374-5.08520.32631500.24812793100
5.0852-40.4410.23631580.2473290599
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)
11.92840.27891.57342.2759-1.57092.3918-0.2727-0.7088-0.135-0.1489-0.33270.3982-1.2026-0.94750.14650.87580.14430.13250.9769-0.06380.6264-20.624815.1913-19.2563
23.441-4.35281.48117.84742.55477.84010.27940.10360.0452-0.224-0.0949-0.2040.52330.3122-0.10750.3411-0.00230.02150.5026-0.00440.4355-15.4116-1.7086-43.2829
32.9043.3962-0.04217.1201-2.60373.4936-0.3893-0.09770.60370.04960.22580.3032-1.2386-0.41440.35510.90220.1920.08230.7346-0.0780.5241-20.812820.9455-33.3393
44.71160.768-3.60386.01091.38044.35930.3712-0.57420.0881-1.4208-0.67620.1235-1.58320.57370.42390.9327-0.1304-0.09510.7894-0.01810.5078-7.307619.0962-11.7162
50.5805-0.0160.50188.0649-2.03654.7909-0.13470.33150.60630.1990.05920.6359-0.4770.10940.14520.4425-0.0025-0.1390.67310.08540.7604-30.23319.7935-75.43
63.0913.76272.46253.89672.34032.6207-0.4442-0.06660.04850.63110.27270.2904-0.48990.26390.2430.870.1217-0.05990.5952-0.00390.7628-17.859534.705-54.5757
78.8666-0.0940.9296.0152-1.89289.2406-0.0353-0.4701-0.06670.46670.43470.2825-0.0450.04-0.4080.570.14050.05920.58810.06630.5081-25.0679.7247-60.6853
85.779-0.48514.54775.9073-1.05866.66-0.19571.23670.4382-0.1439-0.3263-0.90740.31370.88850.46950.7096-0.03090.00210.88530.09750.5545-17.890814.8211-84.7218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 113 )A15 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 213 )A114 - 213
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 279 )A214 - 279
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 337 )A280 - 337
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 113 )B11 - 113
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 231 )B114 - 231
7X-RAY DIFFRACTION7chain 'B' and (resid 232 through 279 )B232 - 279
8X-RAY DIFFRACTION8chain 'B' and (resid 280 through 335 )B280 - 335

+
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