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- PDB-5bqu: Crystal structure of HA17-HA33-Lactulose -

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Basic information

Entry
Database: PDB / ID: 5bqu
TitleCrystal structure of HA17-HA33-Lactulose
Components
  • HA-17
  • HA-33
KeywordsPROTEIN BINDING / Botulinum neurotoxin A / Hemagglutinin / IPTG
Function / homology
Function and homology information


Toxicity of botulinum toxin type A (botA) / Toxicity of botulinum toxin type B (botB) / carbohydrate binding
Similarity search - Function
Hemagglutinin component HA-17 / Clostridium botulinum HA-17 domain / Ricin-type beta-trefoil lectin domain-like / 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
lactulose / HA-33 / HA-17
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.38 Å
AuthorsLee, K. / Lam, K. / Jin, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI091823 United States
CitationJournal: Toxicon / Year: 2015
Title: Inhibiting oral intoxication of botulinum neurotoxin A complex by carbohydrate receptor mimics.
Authors: Lee, K. / Lam, K.H. / Kruel, A.M. / Mahrhold, S. / Perry, K. / Cheng, L.W. / Rummel, A. / Jin, R.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list ...pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HA-33
A: HA-33
C: HA-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9175
Polymers85,2333
Non-polymers6852
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-13 kcal/mol
Surface area30940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.988, 118.667, 161.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTrimer according to Gel filtration

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Components

#1: Protein HA-33 / HA-33 protein / HA33 / HA34 / Non-toxin haemagglutinin HA34


Mass: 34081.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: HA-33, ha33, ha34 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL (DE3) / References: UniProt: Q45871
#2: Protein HA-17 / HA-17 protein / HA17 / Ha17 protein / Non-toxin haemagglutinin HA17


Mass: 17069.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha17, HA-17 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL (DE3) / References: UniProt: Q45878
#3: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-fructofuranose / lactulose /


Type: oligosaccharide, Oligosaccharide / Class: Water retention / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: lactulose
DescriptorTypeProgram
DGalpb1-4DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C6O5>]{[(1+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, 0.1 M magnesium chloride, 5% PEG 8000 / PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.38→47.89 Å / Num. obs: 41291 / % possible obs: 99.4 % / Redundancy: 3.3 % / Net I/σ(I): 14.5
Reflection shellResolution: 2.38→2.51 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.38→47.844 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 2068 5.01 %RANDOM
Rwork0.1889 ---
obs0.191 41263 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→47.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5764 0 46 121 5931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095940
X-RAY DIFFRACTIONf_angle_d1.2298104
X-RAY DIFFRACTIONf_dihedral_angle_d14.5352145
X-RAY DIFFRACTIONf_chiral_restr0.073918
X-RAY DIFFRACTIONf_plane_restr0.0051033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3791-2.43440.30661350.27952575X-RAY DIFFRACTION99
2.4344-2.49530.31831310.26642619X-RAY DIFFRACTION100
2.4953-2.56280.29021200.24882609X-RAY DIFFRACTION100
2.5628-2.63820.29631340.2432596X-RAY DIFFRACTION100
2.6382-2.72330.29651360.23672599X-RAY DIFFRACTION100
2.7233-2.82070.24271470.2282610X-RAY DIFFRACTION100
2.8207-2.93360.25721440.21752595X-RAY DIFFRACTION100
2.9336-3.06710.27261540.20682615X-RAY DIFFRACTION100
3.0671-3.22870.26211310.20962631X-RAY DIFFRACTION100
3.2287-3.4310.25891410.20272604X-RAY DIFFRACTION100
3.431-3.69580.23481490.19142607X-RAY DIFFRACTION99
3.6958-4.06750.23871270.18272644X-RAY DIFFRACTION99
4.0675-4.65570.20261470.14622610X-RAY DIFFRACTION99
4.6557-5.8640.17761480.15462628X-RAY DIFFRACTION98
5.864-47.85350.19371240.17882653X-RAY DIFFRACTION94
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)
12.01611.38692.04832.8531-1.36272.1305-0.36810.2242-0.4685-0.54180.11560.39390.7316-0.13290.33850.48080.08050.01890.298-0.01050.502729.2391368.8863360.1696
22.5713-0.82321.01232.5221-0.34013.11570.0430.14010.2662-0.1388-0.0714-0.0891-0.48490.0647-0.0060.35230.01170.03290.2320.03320.494135.0623371.775365.4497
37.1587-2.724-0.41873.4889-0.15371.68620.96571.999-0.1646-1.08-1.12020.35420.3141-0.1937-0.00710.76410.3938-0.07620.9408-0.05650.591710.2228375.9054338.0065
47.5008-3.14783.02195.3562-2.84115.64030.75330.566-1.6095-0.3513-0.340.19490.539-0.4255-0.2130.6620.1817-0.21740.4672-0.19890.952112.8874369.4939345.6958
50.0203-0.080.04530.03180.00120.01870.12850.735-0.5439-0.5289-0.20330.43280.59060.07320.15971.09010.3413-0.20870.8405-0.3561.036312.5955362.9242338.7343
65.8857-1.36482.26192.2317-2.60613.15870.97881.8615-0.1903-1.5005-0.7953-0.33540.13120.5157-0.05631.10320.68640.06721.3638-0.06370.722921.2261372.7677334.1903
71.5161-0.3992-0.50454.36851.89914.3661-0.0030.0616-0.18710.093-0.0330.06040.3734-0.0510.0430.1811-0.0036-0.03150.19850.02380.41636.4636343.0881371.2158
85.1548-0.54-0.32713.78911.41746.79230.34011.0938-0.0763-0.5204-0.0897-0.1146-0.10790.2898-0.20370.44280.0757-0.02330.5981-0.02710.564745.2439330.7127340.9678
92.59530.7852-0.00533.8245-0.05763.92730.04230.5576-0.0955-0.40580.27620.3550.133-0.357-0.23870.58960.0333-0.10680.6735-0.02790.769435.9886331.115340.3937
102.033-0.9395-0.82941.15480.61944.15060.0895-0.1020.29560.2941-0.045-0.4606-0.50370.81030.07250.4864-0.168-0.0920.3884-0.02890.553149.8796370.7874395.3569
118.43376.977-9.46482.173-9.33142.24810.5461-1.27270.68690.8901-0.7737-0.0576-1.06940.9405-0.29871.1134-0.5594-0.08550.247-0.17180.806247.9758375.5768399.2519
123.31867.475-5.55752.02011.99832.0137-0.3424-0.02140.29-0.17540.54470.7074-0.3602-0.5729-0.45810.7635-0.0172-0.04080.3704-0.03680.58539.1171366.555404.6436
133.0584-0.83340.80971.3752.6432.0465-0.3046-0.5010.28340.7833-0.10770.568-1.41-0.37720.37160.76910.00180.02850.3209-0.03090.605735.7965372.3789394.1369
142.00679.52783.94933.47551.16596.18180.3637-0.53720.27910.82790.0854-0.9626-0.04640.55870.11960.50370.0517-0.10990.3469-0.06590.619847.5898360.2853398.1295
150.6091-0.2439-0.18425.2413-1.64077.322-0.16860.11630.02380.15260.0353-0.2703-0.06910.34030.12670.2179-0.0112-0.05890.2603-0.0260.430643.8007360.437386.6225
162.78524.02820.34916.24740.43820.04080.3615-0.11570.38730.7928-0.0837-0.88770.02250.8721-0.03980.4121-0.0764-0.13660.5321-0.00830.61552.4531365.0206394.1802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 10 through 26 )
2X-RAY DIFFRACTION2chain 'B' and (resid 27 through 150 )
3X-RAY DIFFRACTION3chain 'B' and (resid 151 through 181 )
4X-RAY DIFFRACTION4chain 'B' and (resid 182 through 205 )
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 242 )
6X-RAY DIFFRACTION6chain 'B' and (resid 243 through 294 )
7X-RAY DIFFRACTION7chain 'A' and (resid 10 through 150 )
8X-RAY DIFFRACTION8chain 'A' and (resid 151 through 222 )
9X-RAY DIFFRACTION9chain 'A' and (resid 223 through 294 )
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 35 )
11X-RAY DIFFRACTION11chain 'C' and (resid 36 through 49 )
12X-RAY DIFFRACTION12chain 'C' and (resid 50 through 59 )
13X-RAY DIFFRACTION13chain 'C' and (resid 60 through 85 )
14X-RAY DIFFRACTION14chain 'C' and (resid 86 through 100 )
15X-RAY DIFFRACTION15chain 'C' and (resid 101 through 135 )
16X-RAY DIFFRACTION16chain 'C' and (resid 136 through 145 )

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