[English] 日本語
Yorodumi
- PDB-7fiu: Crystal structure of the DUB domain of Wolbachia cytoplasmic inco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fiu
TitleCrystal structure of the DUB domain of Wolbachia cytoplasmic incompatibility factor CidB from wMel
ComponentsULP_PROTEASE domain-containing protein
KeywordsTOXIN / Wolbachia / cytoplasmic incompatibility / Deubiquitinase
Function / homologyUbiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / proteolysis / Ubiquitin-like protease family profile domain-containing protein
Function and homology information
Biological speciesWolbachia endosymbiont of Drosophila melanogaster (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsXiao, Y.J. / Wang, W. / Chen, X. / Ji, X.Y. / Yang, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81772204 China
CitationJournal: Nat Commun / Year: 2022
Title: Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue.
Authors: Wang, H. / Xiao, Y. / Chen, X. / Zhang, M. / Sun, G. / Wang, F. / Wang, L. / Zhang, H. / Zhang, X. / Yang, X. / Li, W. / Wei, Y. / Yao, D. / Zhang, B. / Li, J. / Cui, W. / Wang, F. / Chen, C. ...Authors: Wang, H. / Xiao, Y. / Chen, X. / Zhang, M. / Sun, G. / Wang, F. / Wang, L. / Zhang, H. / Zhang, X. / Yang, X. / Li, W. / Wei, Y. / Yao, D. / Zhang, B. / Li, J. / Cui, W. / Wang, F. / Chen, C. / Shen, W. / Su, D. / Bai, F. / Huang, J. / Ye, S. / Zhang, L. / Ji, X. / Wang, W. / Wang, Z. / Hochstrasser, M. / Yang, H.
History
DepositionAug 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ULP_PROTEASE domain-containing protein


Theoretical massNumber of molelcules
Total (without water)33,2591
Polymers33,2591
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.110, 60.590, 85.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ULP_PROTEASE domain-containing protein / bacteria factor B


Mass: 33259.301 Da / Num. of mol.: 1 / Fragment: DUB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia endosymbiont of Drosophila melanogaster (bacteria)
Gene: WD_0632 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73HD4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 10mM Nickel (II) Chloride hexahydrate, 100mM TRIS pH 8.5, 20% w/v Polyethylene Glycol Monomethyl Ether 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.84→49.45 Å / Num. obs: 22187 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 36.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.029 / Rrim(I) all: 0.086 / Net I/σ(I): 14.3 / Num. measured all: 190236 / Scaling rejects: 144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.899.11.0631451315900.680.3691.1262.198.6
8.23-49.456.50.05619733020.9960.0220.06126.598.9

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
AutoSolphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 1.84→49.45 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1008 4.55 %
Rwork0.2092 21140 -
obs0.2105 22148 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.28 Å2 / Biso mean: 46.7845 Å2 / Biso min: 21.5 Å2
Refinement stepCycle: final / Resolution: 1.84→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 0 68 2179
Biso mean---49.48 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.940.39691380.31132928306698
1.94-2.060.27931450.24422954309999
2.06-2.220.27991280.23143002313099
2.22-2.440.26831500.20932982313299
2.44-2.790.25311400.213330403180100
2.79-3.520.22071540.207430443198100
3.52-49.450.21961530.19643190334399
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)
15.5562.72660.79512.2792-0.98952.2819-0.4380.504-0.0708-1.44610.1346-0.3683-0.2382-0.43410.25280.63790.05750.04150.3312-0.08060.2422-29.27016.7983-42.3209
24.07060.95282.4653.47940.35746.93680.116-0.32770.0834-0.2247-0.312-0.0932-0.0835-0.10330.19440.29250.0589-0.02550.2722-0.00250.3-23.424810.8151-26.1959
35.89442.16760.67844.9473-0.63286.1801-0.08920.55060.3914-0.34710.1134-0.3983-0.68860.6077-0.05350.38720.0040.00290.37890.03670.2974-1.822817.3214-17.2586
45.8810.67480.13434.6187-0.64284.64530.01020.3495-0.3456-0.2941-0.1535-0.54480.21420.54250.06080.27250.02840.00650.2698-0.01670.2565-2.29364.7991-13.6391
52.99430.39711.2851.7660.00443.13350.0036-0.0998-0.14480.0809-0.03010.0380.0633-0.08420.03040.27990.02430.01430.1873-0.01230.2215-13.37928.4102-4.9517
64.436-0.1921.3113.915-2.04395.8379-0.05540.19610.24080.1266-0.01630.03820.1445-0.0490.09740.42090.0826-0.01030.2862-0.02280.2909-29.054413.6895-32.0616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 837 through 852 )A837 - 852
2X-RAY DIFFRACTION2chain 'A' and (resid 853 through 891 )A853 - 891
3X-RAY DIFFRACTION3chain 'A' and (resid 892 through 952 )A892 - 952
4X-RAY DIFFRACTION4chain 'A' and (resid 953 through 1015 )A953 - 1015
5X-RAY DIFFRACTION5chain 'A' and (resid 1016 through 1085 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1086 through 1121 )A0

+
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