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- PDB-4ouj: Crystal structure of HA33B-Lac -

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Basic information

Entry
Database: PDB / ID: 4ouj
TitleCrystal structure of HA33B-Lac
ComponentsHemagglutinin component HA33
KeywordsTOXIN / Ricin-type beta-trefoil / HA17
Function / homology
Function and homology information


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
alpha-lactose / Hemagglutinin component HA33
Similarity search - Component
Biological speciesClostridium botulinum B1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsLee, K. / Lam, K.-H. / Perry, K. / Rummel, A. / Jin, R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: High-resolution crystal structure of HA33 of botulinum neurotoxin type B progenitor toxin complex.
Authors: Lee, K. / Lam, K.H. / Kruel, A.M. / Perry, K. / Rummel, A. / Jin, R.
History
DepositionFeb 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / 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 / struct_conn / struct_ref_seq_dif / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Hemagglutinin component HA33
B: Hemagglutinin component HA33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9534
Polymers70,2682
Non-polymers6852
Water11,440635
1
A: Hemagglutinin component HA33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4762
Polymers35,1341
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin component HA33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4762
Polymers35,1341
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hemagglutinin component HA33
hetero molecules

B: Hemagglutinin component HA33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9534
Polymers70,2682
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2530 Å2
ΔGint-7 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.819, 36.959, 114.624
Angle α, β, γ (deg.)90.00, 102.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin component HA33


Mass: 35134.090 Da / Num. of mol.: 2 / Mutation: T6V, I288K, T290N, M291I, S292R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum B1 (bacteria) / Strain: serotype B / Gene: CLD_A0071, ha33 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: B1INP8
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Hepes, 5% MPD, 5% (w/v) PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2013
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.46→37.053 Å / Num. all: 374338 / Num. obs: 119409 / % possible obs: 99 % / Observed criterion σ(I): 5 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 15.9
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.413 / % possible all: 97.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LO2

4lo2


Resolution: 1.46→19.801 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 16.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 5954 5.01 %random
Rwork0.1626 ---
obs0.1635 118909 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→19.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 46 635 5215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094688
X-RAY DIFFRACTIONf_angle_d1.2096391
X-RAY DIFFRACTIONf_dihedral_angle_d12.2981657
X-RAY DIFFRACTIONf_chiral_restr0.075730
X-RAY DIFFRACTIONf_plane_restr0.006809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.47660.29091820.27273496X-RAY DIFFRACTION91
1.4766-1.49390.2731990.25273648X-RAY DIFFRACTION98
1.4939-1.51210.27832080.24043707X-RAY DIFFRACTION99
1.5121-1.53130.22612170.22393819X-RAY DIFFRACTION100
1.5313-1.55140.24692090.20993722X-RAY DIFFRACTION100
1.5514-1.57270.2332070.19673728X-RAY DIFFRACTION100
1.5727-1.59510.23031970.19433768X-RAY DIFFRACTION100
1.5951-1.61890.17572060.18323797X-RAY DIFFRACTION100
1.6189-1.64420.20062010.18033736X-RAY DIFFRACTION100
1.6442-1.67110.21612040.1733819X-RAY DIFFRACTION100
1.6711-1.69990.1761740.1653762X-RAY DIFFRACTION100
1.6999-1.73080.19031990.16413755X-RAY DIFFRACTION100
1.7308-1.76410.19062000.15873816X-RAY DIFFRACTION100
1.7641-1.80010.18761930.15593734X-RAY DIFFRACTION100
1.8001-1.83920.18821880.15233828X-RAY DIFFRACTION100
1.8392-1.8820.17392180.15143713X-RAY DIFFRACTION99
1.882-1.9290.20271890.14983802X-RAY DIFFRACTION100
1.929-1.98110.1841950.15573782X-RAY DIFFRACTION100
1.9811-2.03930.15852040.14843800X-RAY DIFFRACTION99
2.0393-2.10510.17562250.14223728X-RAY DIFFRACTION99
2.1051-2.18020.16252020.1493811X-RAY DIFFRACTION100
2.1802-2.26740.16411890.14623781X-RAY DIFFRACTION99
2.2674-2.37040.17992000.14733789X-RAY DIFFRACTION100
2.3704-2.49520.17272010.14723853X-RAY DIFFRACTION100
2.4952-2.65120.18291990.15163805X-RAY DIFFRACTION100
2.6512-2.85530.16841820.15933835X-RAY DIFFRACTION99
2.8553-3.14170.1661980.15923798X-RAY DIFFRACTION99
3.1417-3.59390.17321940.15853824X-RAY DIFFRACTION99
3.5939-4.51910.14631810.14653798X-RAY DIFFRACTION97
4.5191-19.80240.19281930.19363701X-RAY DIFFRACTION92
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)
12.36220.4503-0.10361.7784-0.04741.9635-0.0643-0.12790.0461-0.01770.02270.0402-0.0943-0.15120.04020.0645-0.01090.00420.1637-0.02690.086877.747313.330444.5239
22.01380.17410.40481.11030.07341.74380.0363-0.1166-0.00860.0304-0.0064-0.08140.02720.0933-0.02540.128-0.027-0.01930.058-0.00170.101467.43783.112114.8386
32.5929-0.0163-0.05531.9010.08961.7623-0.09350.0324-0.1126-0.12090.0049-0.03210.1390.34150.02410.0825-0.0150.0120.21180.03830.077428.053613.134140.5538
42.63150.5141-0.06831.78790.06423.6168-0.0241-0.3398-0.17260.1727-0.0042-0.03220.310.09430.05390.14520.04590.00560.25540.09090.1426.37986.485652.3151
52.86010.5217-0.07481.66540.71232.2243-0.0503-0.25440.03760.0656-0.03370.16880.068-0.13760.02720.0658-0.01960.00770.20720.04810.102714.405213.500546.8099
62.57670.0982-0.35561.3910.12181.9625-0.0738-0.16410.23660.0462-0.06070.1126-0.0281-0.02790.03980.0737-0.0395-0.00410.18890.00810.111920.829720.434544.6315
71.81830.3201-0.06531.2166-0.15290.89030.1229-0.26880.04890.0423-0.1068-0.1001-0.15370.0837-0.0190.158-0.04510.01790.0924-0.01170.110137.303829.272917.6212
82.95451.6293-0.22714.2561-0.70912.29980.1378-0.19550.24530.1302-0.02580.2692-0.274-0.249-0.04660.13650.00860.01680.0991-0.00640.094224.776928.633117.2066
91.76660.436-0.08451.9626-0.37682.56880.0351-0.0801-0.0283-0.0585-0.0310.14-0.0069-0.107-0.0210.1221-0.02020.00130.06230.00870.089527.578121.281612.5882
101.98290.3402-0.19881.49190.00851.09490.0307-0.0161-0.2124-0.0468-0.0204-0.14760.07840.1038-0.02230.1333-0.02060.00230.0490.01710.114936.448317.45711.542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 294 )
3X-RAY DIFFRACTION3chain 'B' and (resid 11 through 72 )
4X-RAY DIFFRACTION4chain 'B' and (resid 73 through 96 )
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 123 )
6X-RAY DIFFRACTION6chain 'B' and (resid 124 through 152 )
7X-RAY DIFFRACTION7chain 'B' and (resid 153 through 197 )
8X-RAY DIFFRACTION8chain 'B' and (resid 198 through 217 )
9X-RAY DIFFRACTION9chain 'B' and (resid 218 through 255 )
10X-RAY DIFFRACTION10chain 'B' and (resid 256 through 294 )

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