[English] 日本語
Yorodumi
- PDB-8g33: Activated form of a CDCL long protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g33
TitleActivated form of a CDCL long protein
ComponentsHemolysin
KeywordsTOXIN / Pore-forming toxin / cholesterol-dependent cytolysin like / Elizabethkingia anophelis
Function / homologyThiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / cholesterol binding / : / Hemolysin
Function and homology information
Biological speciesElizabethkingia anophelis Ag1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsJohnstone, B.A. / Christie, M.P. / Morton, C.J. / Parker, M.W.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200102871 Australia
Australian Research Council (ARC)DP160101874 Australia
CitationJournal: To Be Published
Title: Activated form of a CDCL long protein
Authors: Johnstone, B.A. / Christie, M.P. / Morton, C.J. / Tweten, R.K. / Parker, M.W.
History
DepositionFeb 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)55,9061
Polymers55,9061
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.725, 24.451, 300.191
Angle α, β, γ (deg.)90.000, 93.190, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

-
Components

#1: Protein Hemolysin / / Thiol-activated cytolysin


Mass: 55906.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis Ag1 (bacteria)
Gene: ply_2, AYC66_13765, BAY09_14710, NCTC10586_03727 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1T3IZT7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Calcium Acetate Hydrate, 0.1 M Sodium Cacodylate:HCl pH 6.5, 40% (v/v) PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95364 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.49→44.22 Å / Num. obs: 16351 / % possible obs: 99.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 36.31 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.088 / Rrim(I) all: 0.192 / Net I/σ(I): 7.1
Reflection shellResolution: 2.49→2.59 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1703 / CC1/2: 0.557 / Rpim(I) all: 0.496 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→44.22 Å / SU ML: 0.3272 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 816 4.99 %
Rwork0.2075 15529 -
obs0.2096 16345 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.89 Å2
Refinement stepCycle: LAST / Resolution: 2.49→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 0 45 3537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023567
X-RAY DIFFRACTIONf_angle_d0.46994825
X-RAY DIFFRACTIONf_chiral_restr0.0446526
X-RAY DIFFRACTIONf_plane_restr0.0033631
X-RAY DIFFRACTIONf_dihedral_angle_d16.65731330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.650.32891230.25422450X-RAY DIFFRACTION96.22
2.65-2.850.32671310.26012544X-RAY DIFFRACTION99.85
2.85-3.140.29761450.24862594X-RAY DIFFRACTION99.89
3.14-3.590.2881170.21172610X-RAY DIFFRACTION99.82
3.59-4.520.19411270.17692606X-RAY DIFFRACTION99.6
4.52-44.220.21381730.1862725X-RAY DIFFRACTION99.21
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)
12.88958384886-0.0387788530196-0.7231823554661.340586520390.4347295184091.503727775210.07921258381090.0001144212141-0.1132160641890.0503319941949-0.04415462642790.01194895774670.0740693349574-0.199058036436-0.04096900036080.285024045837-0.0273201664067-0.07404932685310.1176071814530.01702171227070.199334148226-21.84365620086.26628373111-53.4509145516
21.69903376867-0.78385975931-1.747506182850.3707117504911.211423780621.96756694650.06143208878070.219988269384-0.0405776064614-0.0432846068203-0.1026198445580.113018647517-0.0474897477608-0.4049551911110.02890002998590.297281441475-0.0443989591979-0.05559422465890.2297779774090.02438719806170.318469584322-32.177124988310.3099161592-47.388692367
33.9154927199-0.449942036078-1.674828927511.579050755711.328002177524.42974697035-0.01925172489450.06141149740490.09440662349150.0756087683230.001907597540750.1203654923340.0705744855248-0.2327574085220.03113968205620.266006818888-0.000871981378223-0.03496666024030.1491094071060.03194023779950.220320961295-45.99772185715.3305404075-0.654974223193
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 77 through 284 )77 - 2841 - 204
22chain 'A' and (resid 285 through 378 )285 - 378205 - 298
33chain 'A' and (resid 379 through 516 )379 - 516299 - 436

+
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