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- PDB-6nal: Crystal Structure of Gram Negative Toxin -

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Basic information

Entry
Database: PDB / ID: 6nal
TitleCrystal Structure of Gram Negative Toxin
ComponentsThiol-activated cytolysinCholesterol-dependent cytolysin
KeywordsTOXIN / CYTOLYSIN
Function / homology
Function and homology information


HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Thiol-activated cytolysin / Thiol-activated cytolysin
Similarity search - Component
Biological speciesDesulfobulbus propionicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMorton, C.J. / Lawrence, S.A. / Parker, M.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP160101874 Australia
CitationJournal: Mbio / Year: 2019
Title: The Structural Basis for a Transition State That Regulates Pore Formation in a Bacterial Toxin.
Authors: Wade, K.R. / Lawrence, S.L. / Farrand, A.J. / Hotze, E.M. / Kuiper, M.J. / Gorman, M.A. / Christie, M.P. / Panjikar, S. / Morton, C.J. / Parker, M.W. / Tweten, R.K.
History
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol-activated cytolysin
B: Thiol-activated cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3545
Polymers106,0212
Non-polymers3323
Water3,639202
1
A: Thiol-activated cytolysin
hetero molecules

B: Thiol-activated cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3545
Polymers106,0212
Non-polymers3323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area4440 Å2
ΔGint-6 kcal/mol
Surface area42830 Å2
MethodPISA
2
A: Thiol-activated cytolysin
hetero molecules

A: Thiol-activated cytolysin
hetero molecules

B: Thiol-activated cytolysin
hetero molecules

B: Thiol-activated cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,70710
Polymers212,0424
Non-polymers6656
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area14340 Å2
ΔGint-35 kcal/mol
Surface area80210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.070, 85.430, 102.440
Angle α, β, γ (deg.)90.000, 101.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thiol-activated cytolysin / Cholesterol-dependent cytolysin


Mass: 53010.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfobulbus propionicus (strain ATCC 33891 / DSM 2032 / 1pr3) (bacteria)
Strain: ATCC 33891 / DSM 2032 / 1pr3 / Gene: Despr_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: E8RGW2, UniProt: A0A7U3YL07*PLUS
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG 6000, 10% Tacsimate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372, 0.97902, 0.97957
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
20.979021
30.979571
ReflectionResolution: 2.2→44.98 Å / Num. obs: 61001 / % possible obs: 100 % / Redundancy: 35.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.049 / Rrim(I) all: 0.314 / Net I/σ(I): 11.4 / Num. measured all: 2147128 / Scaling rejects: 2403
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.257.62.58944890.3581.0012.777100
9.83-44.9842.90.1197260.9980.0180.12199.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→43.445 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.58
RfactorNum. reflection% reflection
Rfree0.2382 2609 4.91 %
Rwork0.1876 --
obs0.1901 53161 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 204.49 Å2 / Biso mean: 59.2977 Å2 / Biso min: 22.74 Å2
Refinement stepCycle: final / Resolution: 2.3→43.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7436 0 51 202 7689
Biso mean--61.11 48.23 -
Num. residues----947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.34190.35421330.319826242757
2.3419-2.38690.38161210.294926692790
2.3869-2.43560.33941520.273426422794
2.4356-2.48860.32381560.262126032759
2.4886-2.54640.25041480.236426202768
2.5464-2.61010.29751330.216726562789
2.6101-2.68070.30591530.222126642817
2.6807-2.75950.28791450.220226472792
2.7595-2.84860.32681360.223926642800
2.8486-2.95040.30581260.223526652791
2.9504-3.06850.30261190.215226432762
3.0685-3.20810.2721200.204726862806
3.2081-3.37720.261340.200526422776
3.3772-3.58870.23591490.191526832832
3.5887-3.86560.26161420.19126342776
3.8656-4.25430.21831180.165827092827
4.2543-4.86920.18571360.138326812817
4.8692-6.13190.1681390.149726882827
6.1319-43.45250.16041490.14327322881

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