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- PDB-6xd4: CDC-like protein -

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ID or keywords:

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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 / : / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Acetate


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


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: SAD

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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

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