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

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Basic information

Entry
Database: PDB / ID: 4owl
TitleCrystal Structure of the Vibrio vulnificus Hemolysin/Cytolysin Beta-Trefoil Lectin with N-Acetyl-D-Lactosamine Bound
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
beta-D-galactopyranose / Cytolysin
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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)1R15AI101977 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: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)110,49818
Polymers107,9417
Non-polymers2,55711
Water9,530529
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)15,5122
Polymers15,4201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8032
Polymers15,4201
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8963
Polymers15,4201
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8963
Polymers15,4201
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8963
Polymers15,4201
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8963
Polymers15,4201
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
G: Cytolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6002
Polymers15,4201
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)326.905, 79.843, 55.607
Angle α, β, γ (deg.)90.000, 95.710, 90.000
Int Tables number5
Space group name H-MC121

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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: Polysaccharide
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 100 mM TRIS, pH 8.25, 6% PEG 8000, 2 mM N-acetyl-D-lactosamine: 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: 2.1→100 Å / Num. obs: 83123 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.113 / Χ2: 1.993 / Net I/av σ(I): 23.955 / Net I/σ(I): 9.5 / Num. measured all: 375224
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.184.30.69382500.80199.9
2.18-2.264.70.55982670.961100
2.26-2.374.60.48683110.994100
2.37-2.494.70.31182911.137100
2.49-2.654.70.22582931.41999.9
2.65-2.854.60.17682811.78799.9
2.85-3.144.60.12983042.55399.9
3.14-3.594.50.09583173.26599.8
3.59-4.524.30.06783453.79899.8
4.52-1004.20.05784643.49499.2

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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
RefinementResolution: 2.1→40.162 Å / FOM work R set: 0.8897 / SU ML: 0.17 / σ(F): 1.37 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 4152 5 %
Rwork0.1621 78956 -
obs0.1634 83108 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.63 Å2 / Biso mean: 52.05 Å2 / Biso min: 14.31 Å2
Refinement stepCycle: final / Resolution: 2.1→40.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7017 0 347 529 7893
Biso mean--76.35 45.83 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137332
X-RAY DIFFRACTIONf_angle_d1.2829975
X-RAY DIFFRACTIONf_chiral_restr0.061128
X-RAY DIFFRACTIONf_plane_restr0.0061285
X-RAY DIFFRACTIONf_dihedral_angle_d12.7432563
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 (%)
2.0999-2.12380.24261300.206825942724100
2.1238-2.14880.21081260.184526502776100
2.1488-2.1750.22251170.170526252742100
2.175-2.20250.1781220.165126322754100
2.2025-2.23150.19521220.179826602782100
2.2315-2.26210.27171130.219926172730100
2.2621-2.29440.23241400.194926132753100
2.2944-2.32860.21841630.171626172780100
2.3286-2.3650.19351360.160226432779100
2.365-2.40380.19891300.156426182748100
2.4038-2.44520.19961430.154526182761100
2.4452-2.48970.17731630.149526172780100
2.4897-2.53750.18711240.152826412765100
2.5375-2.58930.1981370.155725812718100
2.5893-2.64560.19041520.150426612813100
2.6456-2.70710.21621660.163125612727100
2.7071-2.77480.18511390.154526662805100
2.7748-2.84980.2011290.162326182747100
2.8498-2.93370.19371280.158426502778100
2.9337-3.02830.18551270.160526212748100
3.0283-3.13650.19331510.16826192770100
3.1365-3.26210.21021530.170226482801100
3.2621-3.41040.21441510.177125822733100
3.4104-3.59010.21921260.173326662792100
3.5901-3.81490.17911460.159126292775100
3.8149-4.10920.1531390.14826362775100
4.1092-4.52220.13661440.130226482792100
4.5222-5.17540.1411390.13282646278599
5.1754-6.5160.19161550.16732656281199
6.516-40.16960.19921410.19252723286499
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)
13.29970.5970.52941.4170.83781.19790.071-0.27210.2186-0.0828-0.3360.5299-0.0753-0.49120.14580.3119-0.0287-0.08071.1586-0.1320.9352329.354183.502269.9772
23.04270.1646-0.47572.14540.4951.08540.1890.6227-0.7138-0.2538-0.29080.439-0.1261-0.66090.03840.32370.0218-0.16091.0018-0.12960.8753340.802662.947847.5926
34.62561.30161.32363.42430.92953.5197-0.15061.1207-0.6199-0.55320.18530.36780.0728-0.2916-0.02980.3582-0.0334-0.12920.5623-0.15140.5283371.85956.334640.9717
42.84290.75670.11773.10021.54263.63170.04260.09630.0192-0.2681-0.0120.0385-0.2540.0419-0.03090.30.02870.01040.1085-0.01380.1616398.024270.640954.2212
52.4239-0.3049-0.93113.84641.06993.2206-0.004-0.09220.04940.09260.0262-0.07-0.05810.1609-0.04210.23670.0019-0.01010.13270.00620.1158400.380991.169578.9005
64.2668-0.4599-0.65633.20750.54223.63870.218-0.18710.25450.0261-0.20670.3748-0.2016-0.23530.01620.2653-0.02520.04040.2015-0.05510.2425376.5995105.289295.7695
73.4470.45330.76540.37070.73521.48550.1377-0.8030.78110.2125-0.55490.8047-0.0463-1.11510.19140.30950.00390.02470.9613-0.26820.9475345.092101.667391.7562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA337 - 503
2X-RAY DIFFRACTION2chain BB337 - 467
3X-RAY DIFFRACTION3chain CC337 - 467
4X-RAY DIFFRACTION4chain DD335 - 471
5X-RAY DIFFRACTION5chain EE336 - 467
6X-RAY DIFFRACTION6chain FF337 - 467
7X-RAY DIFFRACTION7chain GG337 - 467

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