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- PDB-1xez: Crystal Structure Of The Vibrio Cholerae Cytolysin (HlyA) Pro-Tox... -

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Basic information

Entry
Database: PDB / ID: 1xez
TitleCrystal Structure Of The Vibrio Cholerae Cytolysin (HlyA) Pro-Toxin With Octylglucoside Bound
Componentshemolysin
KeywordsTOXIN / Pore-forming toxin / hemolysin / cytolysin / pro-toxin / water-soluble monomer / beta-prism / beta-trefoil
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / carbohydrate binding / host cell plasma membrane / extracellular region / membrane / identical protein binding
Similarity search - Function
Leukocidin/Hemolysin toxin, cytolysin domain / Hemolytic toxin, N-terminal domain / Leukocidin/Hemolysin toxin, pre-stem domain / Porin MspA ribbon fold / Hemolytic toxin, N-terminal / Hemolytic toxin, N-terminal domain superfamily / Hemolysin, pre-stem domain / Hemolytic toxin N terminal / Hemolysin, beta-prism lectin / Beta-prism lectin ...Leukocidin/Hemolysin toxin, cytolysin domain / Hemolytic toxin, N-terminal domain / Leukocidin/Hemolysin toxin, pre-stem domain / Porin MspA ribbon fold / Hemolytic toxin, N-terminal / Hemolytic toxin, N-terminal domain superfamily / Hemolysin, pre-stem domain / Hemolytic toxin N terminal / Hemolysin, beta-prism lectin / Beta-prism lectin / Leukocidin-like / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Jacalin-like lectin domain / Translation Initiation Factor IF3 / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain superfamily / Ricin-type beta-trefoil / Other non-globular / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Distorted Sandwich / Special / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsOlson, R. / Gouaux, E.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of the Vibrio cholerae Cytolysin (VCC) Pro-toxin and its Assembly into a Heptameric Transmembrane Pore
Authors: Olson, R. / Gouaux, E.
History
DepositionSep 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE THE SEQUENCE OF THE PROTEIN IS NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE DATABASE. ...SEQUENCE THE SEQUENCE OF THE PROTEIN IS NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE DATABASE. RESIDUES -4 TO 0 ARE CLONING ARTIFACTS. RESIDUES 119 AND 123 WERE MUTATED FROM ARG TO ALA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9432
Polymers79,6511
Non-polymers2921
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.211, 97.321, 135.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hemolysin / / Cytolysin


Mass: 79650.688 Da / Num. of mol.: 1 / Mutation: R119A, R123A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 El Tor 8731 / Gene: HlyA / Plasmid: pHIS-parallel2 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (Novagen) / References: UniProt: P09545
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, ethylene glycol, b-octylglucoside, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.97945, 0.97911, 0.97244
SYNCHROTRONNSLS X4A21.03917
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 18, 2002
ADSC QUANTUM 42CCDNov 14, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) Double CrystalMADMx-ray1
2Si(111) Double CrystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979111
30.972441
41.039171
ReflectionResolution: 2.3→30 Å / Num. all: 45034 / Num. obs: 45034 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.36 % / Biso Wilson estimate: 37.276 Å2 / Rsym value: 0.082 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2968 / Rsym value: 0.355 / % possible all: 61.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Isotropic thermal model: Overall anisotropic B value / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 4514 -Random
Rwork0.207 ---
all0.23 44780 --
obs0.23 44780 92.7 %-
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å20 Å2
2---5.337 Å20 Å2
3---1.618 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5065 0 20 300 5385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_dihedral_angle_d26.1

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