[English] 日本語
Yorodumi
- PDB-6xd4: CDC-like protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xd4
TitleCDC-like protein
ComponentsHemolysin
KeywordsTOXIN / CDC-like / Pore-forming / Bacterial
Function / homologyThiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / cholesterol binding / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETATE ION / Hemolysin
Function and homology information
Biological speciesElizabethkingia anophelis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMorton, C.J. / Parker, M.W. / Lawrence, S.L. / Johnstone, B.A. / Tweten, R.K.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200102871 Australia
Australian Research Council (ARC)DP160101874 Australia
CitationJournal: Mbio / Year: 2020
Title: A Key Motif in the Cholesterol-Dependent Cytolysins Reveals a Large Family of Related Proteins.
Authors: Evans, J.C. / Johnstone, B.A. / Lawrence, S.L. / Morton, C.J. / Christie, M.P. / Parker, M.W. / Tweten, R.K.
History
DepositionJun 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3715
Polymers58,1711
Non-polymers2004
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-3 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.740, 121.740, 88.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Hemolysin / Bacterial Pore-forming protein


Mass: 58170.758 Da / Num. of mol.: 1 / Fragment: UNP residues 24-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis (bacteria) / Gene: AYC66_13765, BAY09_14710, BAY10_16345 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1T3IZT7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.9458.2Cubic
22.9458.1Cubic
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2941vapor diffusion, hanging drop72.8 M sodium acetate
2942vapor diffusion, hanging drop72.8 M sodium acetate

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX210.9636
SYNCHROTRONAustralian Synchrotron MX220.9537
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDAug 12, 2016
DECTRIS EIGER X 16M2PIXELOct 13, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.96361
20.95371
Reflection

Entry-ID: 6XD4 / Rpim(I) all: 0.031 / % possible obs: 97.34 %

Resolution (Å)Num. obsRedundancy (%)Biso Wilson estimate (Å2)CC1/2CC starRmerge(I) obsRrim(I) allDiffraction-IDNet I/σ(I)
2.09-20.153980114.845.870.99910.1460.161114.8
2.27-46.433068726.441.26217
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2CC starDiffraction-ID% possible allRpim(I) all
2.1-2.17515.11.8931990.6430.8341100
2.27-2.3522.5722262272.990.315

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
HKL-2000data scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→43.04 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 3766 5.05 %
Rwork0.202 70775 -
obs0.2042 39544 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 226.49 Å2 / Biso mean: 65.6055 Å2 / Biso min: 30.53 Å2
Refinement stepCycle: final / Resolution: 2.1→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 22 99 3775
Biso mean--52.39 50.8 -
Num. residues----458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.130.38771440.372526152759
2.13-2.150.36071420.356826472789
2.15-2.180.38061420.339626212763
2.18-2.220.35471420.338326332775
2.22-2.250.32671350.336226022737
2.25-2.280.36641420.328526082750
2.28-2.320.33961410.318226432784
2.32-2.360.34111390.278625782717
2.36-2.40.30591460.283326422788
2.4-2.450.33931360.266226222758
2.45-2.50.26051390.257826032742
2.5-2.550.29241380.251226592797
2.55-2.610.28611400.236325942734
2.61-2.680.31611370.236626082745
2.68-2.750.33291370.223226102747
2.75-2.830.29871430.210926522795
2.83-2.920.25041350.216126182753
2.92-3.030.22791420.207126402782
3.03-3.150.26361370.192325972734
3.15-3.290.25411420.184426532795
3.29-3.470.19221360.178325912727
3.47-3.680.26791420.178626182760
3.68-3.970.19451450.170226372782
3.97-4.370.17411350.153525872722
4.37-50.21611380.140626432781
5-6.290.18761390.176926152754
6.3-43.040.24751320.202926392771

+
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