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- PDB-4owj: Crystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Be... -

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Basic information

Entry
Database: PDB / ID: 4owj
TitleCrystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Beta-Trefoil Lectin
ComponentsCytolysin
KeywordsTOXIN / lectin / pore-forming toxin / Beta-trefoil / R-type lectin
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / carbohydrate binding / extracellular region
Similarity search - Function
Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKaus, K. / Olson, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI101977 United States
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Glycan Specificity of the Vibrio vulnificus Hemolysin Lectin Outlines Evolutionary History of Membrane Targeting by a Toxin Family.
Authors: Kaus, K. / Lary, J.W. / Cole, J.L. / Olson, R.
History
DepositionFeb 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Derived calculations
Revision 1.3Oct 7, 2015Group: Other
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 1, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.method_details
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytolysin
B: Cytolysin
C: Cytolysin
D: Cytolysin
E: Cytolysin
F: Cytolysin
G: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,23021
Polymers107,9417
Non-polymers1,28914
Water16,484915
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6043
Polymers15,4201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6043
Polymers15,4201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6043
Polymers15,4201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6043
Polymers15,4201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6043
Polymers15,4201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6043
Polymers15,4201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
G: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6043
Polymers15,4201
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.833, 118.214, 149.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsDomain exists in a monomer-heptamer equilibrium in solution. Similar to related pore-forming toxins, full-length toxin likely exists as a monomer until assembling on the cell membrane.

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Components

#1: Protein
Cytolysin


Mass: 15420.086 Da / Num. of mol.: 7 / Fragment: UNP residues 338-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV2_0404,vvhA / Plasmid: pNGFP-BC / Production host: Escherichia coli (E. coli) / Strain (production host): NEB SHuffle T7 Express / References: UniProt: P19247
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 100 mM TRIS, pH 8.25, 6% PEG 8000; Cryoprotected in 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 91312 / % possible obs: 100 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.175 / Χ2: 1.786 / Net I/av σ(I): 17.292 / Net I/σ(I): 4.8 / Num. measured all: 756224
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.078.10.6989990.627100
2.07-2.158.70.56190330.68100
2.15-2.258.50.45990040.776100
2.25-2.378.60.38190890.877100
2.37-2.528.90.29990471.121100
2.52-2.718.50.24990841.451100
2.71-2.998.50.20491092.013100
2.99-3.428.20.15691682.894100
3.42-4.317.70.11792083.79499.9
4.31-507.20.10695714.13299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
HKL-2000704xdata reduction
PHASER2.5.5phasing
PHENIX1.8.4-1496refinement
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.07 Å / FOM work R set: 0.852 / SU ML: 0.17 / σ(F): 1.37 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 4566 5.01 %
Rwork0.1663 86630 -
obs0.1681 91196 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.86 Å2 / Biso mean: 36.54 Å2 / Biso min: 19.25 Å2
Refinement stepCycle: final / Resolution: 2→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7023 0 196 915 8134
Biso mean--59.66 42.75 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017241
X-RAY DIFFRACTIONf_angle_d1.1789815
X-RAY DIFFRACTIONf_chiral_restr0.0491068
X-RAY DIFFRACTIONf_plane_restr0.0051273
X-RAY DIFFRACTIONf_dihedral_angle_d13.2872521
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9999-2.02270.22261480.20192802295099
2.0227-2.04650.27861680.198528953063100
2.0465-2.07140.25221410.194328282969100
2.0714-2.09760.24491420.188128562998100
2.0976-2.12520.23131640.184828352999100
2.1252-2.15430.20611220.176229123034100
2.1543-2.18510.22221460.180128442990100
2.1851-2.21770.22571370.176828582995100
2.2177-2.25240.21081630.177628513014100
2.2524-2.28930.21881410.172428803021100
2.2893-2.32880.23481600.174228503010100
2.3288-2.37110.23851480.167729003048100
2.3711-2.41670.20241670.164828172984100
2.4167-2.4660.2151420.162929103052100
2.466-2.51960.22081570.162528503007100
2.5196-2.57820.19381630.157628383001100
2.5782-2.64270.20561640.158728613025100
2.6427-2.71410.21511670.158828863053100
2.7141-2.7940.20661360.158828903026100
2.794-2.88410.2121410.166629043045100
2.8841-2.98720.2081600.160828723032100
2.9872-3.10670.17241490.163728993048100
3.1067-3.24810.18821450.165728993044100
3.2481-3.41920.20341460.169629183064100
3.4192-3.63330.20051570.176229023059100
3.6333-3.91350.20841610.166628993060100
3.9135-4.30690.15611350.142329483083100
4.3069-4.92890.16761650.137429503115100
4.9289-6.20560.16111520.162629953147100
6.2056-38.07670.22911790.19833081326099
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)
12.17970.925-0.91735.5024-0.39682.3264-0.20880.0827-0.0826-0.41760.1291-0.32920.33920.1810.05370.25890.03110.03910.20060.00780.190479.531133.5266113.007
21.37180.0819-0.1131.5864-0.28493.6699-0.0101-0.0304-0.01350.0796-0.0115-0.11830.38230.2993-0.00670.38850.10230.06540.22990.00460.216577.3514107.2678131.6386
31.5552-0.1712-0.20322.60022.13845.97350.01240.0901-0.1173-0.0493-0.1540.02470.66730.20350.12530.40910.090.03980.25640.00790.211277.805106.0038163.6933
41.05190.9374-0.26938.55842.22643.61890.0611-0.13620.00730.8122-0.1229-0.03430.25120.20820.07430.2261-0.01330.00030.24530.0220.230281.1305129.9437185.1717
51.88550.4885-0.1825.3952-1.8992.65510.0595-0.115-0.06850.4354-0.1161-0.0548-0.1724-0.08350.05870.2393-0.01880.01190.225-0.03810.192482.7034161.5943179.8036
61.36150.5570.40121.49580.04374.4678-0.10880.02050.0679-0.06320.03330.066-0.3926-0.09120.0750.29370.0194-0.05940.2347-0.01920.240683.353176.9585151.4581
71.2269-0.3126-0.04694.2021.89214.1271-0.04050.00350.05990.05580.1804-0.3847-0.06210.2893-0.08670.1867-0.0498-0.0130.23440.00620.208582.6212164.2996121.8471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA337 - 502
2X-RAY DIFFRACTION2chain BB337 - 467
3X-RAY DIFFRACTION3chain CC337 - 467
4X-RAY DIFFRACTION4chain DD337 - 467
5X-RAY DIFFRACTION5chain EE337 - 467
6X-RAY DIFFRACTION6chain FF337 - 468
7X-RAY DIFFRACTION7chain GG337 - 467

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