[English] 日本語
Yorodumi
- PDB-6gzu: Structure of Chlamydia abortus effector protein ChlaDUB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gzu
TitleStructure of Chlamydia abortus effector protein ChlaDUB
ComponentsConserved membrane protein
KeywordsTRANSFERASE / Enzyme / CE clan / Acetyltransferase
Function / homology
Function and homology information


: / cysteine-type peptidase activity / host cell / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / extracellular region
Similarity search - Function
Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ulp1 protease family, C-terminal catalytic domain protein / Conserved membrane protein
Similarity search - Component
Biological speciesChlamydia abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsPruneda, J.N. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council724804 United Kingdom
CitationJournal: Nat Microbiol / Year: 2018
Title: A Chlamydia effector combining deubiquitination and acetylation activities induces Golgi fragmentation.
Authors: Pruneda, J.N. / Bastidas, R.J. / Bertsoulaki, E. / Swatek, K.N. / Santhanam, B. / Clague, M.J. / Valdivia, R.H. / Urbe, S. / Komander, D.
History
DepositionJul 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conserved membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1393
Polymers30,9821
Non-polymers1582
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.337, 41.775, 44.209
Angle α, β, γ (deg.)94.72, 102.17, 101.23
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Conserved membrane protein


Mass: 30981.873 Da / Num. of mol.: 1 / Fragment: UNP residues 108-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia abortus (bacteria) / Gene: CAB683 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5L5G1, UniProt: A0A658S2I9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris (pH 7.0), 0.2 M Calcium acetate, 20% PEG 3000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.47→42.86 Å / Num. obs: 45047 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.4
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HAG

5hag


Resolution: 1.47→42.855 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.81
RfactorNum. reflection% reflection
Rfree0.1816 2421 5.38 %
Rwork0.1515 --
obs0.1532 45029 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→42.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 7 192 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142007
X-RAY DIFFRACTIONf_angle_d1.5572751
X-RAY DIFFRACTIONf_dihedral_angle_d12.53726
X-RAY DIFFRACTIONf_chiral_restr0.099311
X-RAY DIFFRACTIONf_plane_restr0.009353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.26731390.23832469X-RAY DIFFRACTION94
1.5-1.53260.28121290.21352474X-RAY DIFFRACTION94
1.5326-1.56830.22671320.18832455X-RAY DIFFRACTION95
1.5683-1.60750.20071410.16422495X-RAY DIFFRACTION95
1.6075-1.6510.18571430.15782419X-RAY DIFFRACTION95
1.651-1.69960.20121740.1452459X-RAY DIFFRACTION95
1.6996-1.75440.17891430.13532505X-RAY DIFFRACTION96
1.7544-1.81710.1831360.14092519X-RAY DIFFRACTION96
1.8171-1.88990.20011260.14252477X-RAY DIFFRACTION96
1.8899-1.97590.17741290.13242522X-RAY DIFFRACTION97
1.9759-2.08010.16981540.14272521X-RAY DIFFRACTION97
2.0801-2.21040.2031430.14872515X-RAY DIFFRACTION97
2.2104-2.3810.20051410.14752540X-RAY DIFFRACTION97
2.381-2.62060.18751570.15252554X-RAY DIFFRACTION98
2.6206-2.99970.20361200.16142568X-RAY DIFFRACTION98
2.9997-3.7790.16241600.1512556X-RAY DIFFRACTION99
3.779-42.87350.15911540.14612560X-RAY DIFFRACTION99

+
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://pdbjlc1.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