[English] 日本語
Yorodumi
- PDB-6yhl: Crystal structure of CNFy from Yersinia pseudotuberculosis - N-te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yhl
TitleCrystal structure of CNFy from Yersinia pseudotuberculosis - N-terminal fragment comprising residues 1-704
ComponentsCytotoxic necrotizing factor
KeywordsTOXIN / CNF / cytotoxic necrotizing factor / deamidase / RhoA modification / RhoA activation / putative ADP-ribosyltransferase
Function / homology
Function and homology information


Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Dermonecrotic toxin, N-terminal domain / Cytotoxic necrotizing factor-like, catalytic
Similarity search - Domain/homology
Cytotoxic necrotizing factor
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.277 Å
Model detailsStructure comprises residues 1-1014, active site cysteine 866 has been mutated to serine
AuthorsLukat, P. / Gazdag, E.M. / Heidler, T.V. / Blankenfeldt, W.
CitationJournal: Embo J. / Year: 2021
Title: Crystal structure of bacterial cytotoxic necrotizing factor CNF Y reveals molecular building blocks for intoxication.
Authors: Chaoprasid, P. / Lukat, P. / Muhlen, S. / Heidler, T. / Gazdag, E.M. / Dong, S. / Bi, W. / Ruter, C. / Kirchenwitz, M. / Steffen, A. / Jansch, L. / Stradal, T.E.B. / Dersch, P. / Blankenfeldt, W.
History
DepositionMar 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytotoxic necrotizing factor
B: Cytotoxic necrotizing factor


Theoretical massNumber of molelcules
Total (without water)160,8052
Polymers160,8052
Non-polymers00
Water00
1
A: Cytotoxic necrotizing factor


Theoretical massNumber of molelcules
Total (without water)80,4031
Polymers80,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytotoxic necrotizing factor


Theoretical massNumber of molelcules
Total (without water)80,4031
Polymers80,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.425, 99.896, 131.357
Angle α, β, γ (deg.)90.000, 95.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 217 or (resid 218...
21(chain B and (resid 3 through 141 or (resid 142...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASNASN(chain A and (resid 3 through 217 or (resid 218...AA3 - 2173 - 217
12LYSLYSLYSLYS(chain A and (resid 3 through 217 or (resid 218...AA218218
13ASNASNPHEPHE(chain A and (resid 3 through 217 or (resid 218...AA3 - 6973 - 697
21ASNASNASNASN(chain B and (resid 3 through 141 or (resid 142...BB3 - 1413 - 141
22LYSLYSALAALA(chain B and (resid 3 through 141 or (resid 142...BB142 - 143142 - 143
23METMETPROPRO(chain B and (resid 3 through 141 or (resid 142...BB1 - 6981 - 698
24METMETPROPRO(chain B and (resid 3 through 141 or (resid 142...BB1 - 6981 - 698
25METMETPROPRO(chain B and (resid 3 through 141 or (resid 142...BB1 - 6981 - 698
26METMETPROPRO(chain B and (resid 3 through 141 or (resid 142...BB1 - 6981 - 698

-
Components

#1: Protein Cytotoxic necrotizing factor


Mass: 80402.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CNFy from Yersinia pseudotuberculosis - N-terminal fragment comprising residues 1-704
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: cnf / Plasmid: pET28c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0N9JNY6

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.8367.91
2
Crystal grow
Temperature (K)Crystal-IDMethodDetailsPH range
2931vapor diffusion0.2 M ammonium acetate, 28-32 % (w/v) PEG 4000, 0.1 M tri-sodium citrate pH 5.9 - 6.25.9 - 6.2
2932vapor diffusion19-20 % ammonium sulfate, 19-21 % (w/v) PEG 5000 MME, 0.1 M Tis/HCl pH 7.3-7.97.3 - 7.9

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA11
SYNCHROTRONBESSY 14.120.979
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M-F1PIXELAug 27, 2014
DECTRIS PILATUS 6M2PIXELJul 31, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
ReflectionResolution: 3.277→99.9 Å / Num. obs: 37569 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 96.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 7.1 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.28-3.450.79354590.8020.3190.856100
10.36-99.90.022124610.0090.02399.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.277→54.679 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.38
RfactorNum. reflection% reflection
Rfree0.2646 1888 5.03 %
Rwork0.2405 --
obs0.2417 37535 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 202.54 Å2 / Biso mean: 97.22 Å2 / Biso min: 34.66 Å2
Refinement stepCycle: final / Resolution: 3.277→54.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11022 0 0 0 11022
Num. residues----1393
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6390X-RAY DIFFRACTION11.458TORSIONAL
12B6390X-RAY DIFFRACTION11.458TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.277-3.36510.40351470.34452722100
3.3651-3.46410.38631540.33412697100
3.4641-3.57590.39781460.30952733100
3.5759-3.70370.3341530.29772701100
3.7037-3.8520.30071460.28322750100
3.852-4.02720.31251460.28642713100
4.0272-4.23950.30191350.2672749100
4.2395-4.5050.2431380.22912744100
4.505-4.85260.24231380.22052743100
4.8526-5.34060.24771460.22442743100
5.3406-6.11250.28081530.24852754100
6.1125-7.69770.23321320.23362791100
7.6977-54.6790.18961540.1727280799

+
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