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- PDB-1ybi: Crystal structure of HA33A, a neurotoxin-associated protein from ... -

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Basic information

Entry
Database: PDB / ID: 1ybi
TitleCrystal structure of HA33A, a neurotoxin-associated protein from Clostridium botulinum type A
Componentsnon-toxin haemagglutinin HA34
KeywordsTOXIN / BETA-TREFOIL
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
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsArndt, J.W. / Gu, J. / Jaroszewski, L. / Schwarzenbacher, R. / Hanson, M. / Lebeda, F.J. / Stevens, R.C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Structure of the Neurotoxin-associated Protein HA33/A from Clostridium botulinum Suggests a Reoccurring beta-Trefoil Fold in the Progenitor Toxin Complex.
Authors: Arndt, J.W. / Gu, J. / Jaroszewski, L. / Schwarzenbacher, R. / Hanson, M.A. / Lebeda, F.J. / Stevens, R.C.
History
DepositionDec 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: non-toxin haemagglutinin HA34
B: non-toxin haemagglutinin HA34


Theoretical massNumber of molelcules
Total (without water)66,5042
Polymers66,5042
Non-polymers00
Water10,160564
1
A: non-toxin haemagglutinin HA34


Theoretical massNumber of molelcules
Total (without water)33,2521
Polymers33,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: non-toxin haemagglutinin HA34


Theoretical massNumber of molelcules
Total (without water)33,2521
Polymers33,2521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.084, 146.595, 35.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein non-toxin haemagglutinin HA34 / HA33A / HA33/A


Mass: 33251.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridium botulinum (bacteria) / Strain: SEROTYPE A, HALL STRAIN / References: UniProt: Q45871
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 15% isopropanol, 200 mM Li2SO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9179 / Wavelength: 0.9179 Å
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 88654 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.066 / Net I/σ(I): 13.6
Reflection shellResolution: 1.5→1.539 Å / Mean I/σ(I) obs: 3.7 / Num. unique all: 88654 / Rsym value: 0.299 / % possible all: 78.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1QXM

1qxm


Resolution: 1.5→21.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.297 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.085 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19445 3820 4.9 %RANDOM
Rwork0.16771 ---
obs0.16904 73397 87.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.526 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 0 564 5241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224777
X-RAY DIFFRACTIONr_bond_other_d0.0060.024100
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.9156518
X-RAY DIFFRACTIONr_angle_other_deg0.7439564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22225.479261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57215800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7711521
X-RAY DIFFRACTIONr_chiral_restr0.0780.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02968
X-RAY DIFFRACTIONr_nbd_refined0.2170.2882
X-RAY DIFFRACTIONr_nbd_other0.1890.24080
X-RAY DIFFRACTIONr_nbtor_refined0.180.22398
X-RAY DIFFRACTIONr_nbtor_other0.0830.22523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2428
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0240.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.250
X-RAY DIFFRACTIONr_mcbond_it0.8581.53002
X-RAY DIFFRACTIONr_mcbond_other0.1651.51150
X-RAY DIFFRACTIONr_mcangle_it1.06824637
X-RAY DIFFRACTIONr_scbond_it1.86332198
X-RAY DIFFRACTIONr_scangle_it2.5634.51881
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 264 -
Rwork0.186 4857 -
obs--79.69 %

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