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- PDB-2e4m: Crystal structure of hemagglutinin subcomponent complex (HA-33/HA... -

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Basic information

Entry
Database: PDB / ID: 2e4m
TitleCrystal structure of hemagglutinin subcomponent complex (HA-33/HA-17) from Clostridium botulinum serotype D strain 4947
Components
  • HA-17
  • Main hemagglutinin component
KeywordsTOXIN / Clostridium botulinum / botulinum toxin / hemagglutinin subcomponent complex
Function / homology
Function and homology information


carbohydrate binding / extracellular region
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
Hemagglutinin component HA33 / Main hemagglutinin component type C / Hemagglutinin component HA-17 type D
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHasegawa, K. / Watanabe, T. / Suzuki, T. / Yamano, A. / Niwa, K. / Ohyama, T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: A Novel Subunit Structure of Clostridium botulinum Serotype D Toxin Complex with Three Extended Arms
Authors: Hasegawa, K. / Watanabe, T. / Suzuki, T. / Yamano, A. / Oikawa, T. / Sato, Y. / Kouguchi, H. / Yoneyama, T. / Niwa, K. / Ikeda, T. / Ohyama, T.
History
DepositionDec 13, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE The difference between the sequence and the SEQRES occurs naturally in serotype D of this ...SEQUENCE The difference between the sequence and the SEQRES occurs naturally in serotype D of this organism. These residues refer from EMBL/GB AB037920; BAA90659.1.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Main hemagglutinin component
B: Main hemagglutinin component
C: HA-17


Theoretical massNumber of molelcules
Total (without water)84,3073
Polymers84,3073
Non-polymers00
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-17 kcal/mol
Surface area28980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)239.132, 239.132, 100.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

DetailsThe biological assembly is a trimer

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Components

#1: Protein Main hemagglutinin component / HA 33 kDa subunit / HA1 / HA-33


Mass: 33796.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridium botulinum (bacteria) / Strain: SEROTYPE D STRAIN 4947 / References: UniProt: P46084, UniProt: K4Q2R6*PLUS
#2: Protein HA-17


Mass: 16714.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium botulinum (bacteria) / Strain: SEROTYPE D STRAIN 4947 / References: UniProt: Q9LBR4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 7% PEG 8000, 0.1M MES, 0.1M Magnesium Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSPring-8 BL26B221
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS VII1IMAGE PLATEApr 21, 2006RIGAKU MaxScreen
RIGAKU JUPITER 2102CCDJul 19, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 1.85→119.52 Å / Num. obs: 92648 / % possible obs: 99.8 % / Biso Wilson estimate: 25.8 Å2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QXM

1qxm


Resolution: 1.85→49.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.601 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; CNS 1.1 was also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.22879 4626 5 %RANDOM
Rwork0.19372 ---
obs0.19553 87820 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5913 0 0 718 6631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226041
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9148238
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0695710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36325.91335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.202151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4611520
X-RAY DIFFRACTIONr_chiral_restr0.120.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024649
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.22811
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24137
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2612
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9621.53676
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57825820
X-RAY DIFFRACTIONr_scbond_it2.28532811
X-RAY DIFFRACTIONr_scangle_it3.3534.52418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 335 -
Rwork0.251 6468 -
obs--100 %

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