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- PDB-4en6: Crystal structure of HA70 (HA3) subcomponent of Clostridium botul... -

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Basic information

Entry
Database: PDB / ID: 4en6
TitleCrystal structure of HA70 (HA3) subcomponent of Clostridium botulinum type C progenitor toxin in complex with alpha 2-3-sialyllactose
Components(Hemagglutinin components HA-22/23/53) x 2
KeywordsSUGAR BINDING PROTEIN / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Jelly Rolls - #1080 / Jelly Rolls - #1090 / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / Beta Complex / Jelly Rolls ...Jelly Rolls - #1080 / Jelly Rolls - #1090 / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / Beta Complex / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hemagglutinin components HA-70 type C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsYamashita, S. / Yoshida, H. / Tonozuka, T. / Nishikawa, A. / Kamitori, S.
Citation
Journal: Febs Lett. / Year: 2012
Title: Carbohydrate recognition mechanism of HA70 from Clostridium botulinum deduced from X-ray structures in complexes with sialylated oligosaccharides
Authors: Yamashita, S. / Yoshida, H. / Uchiyama, N. / Nakakita, Y. / Nakakita, S. / Tonozuka, T. / Oguma, K. / Nishikawa, A. / Kamitori, S.
#1: Journal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the HA3 subcomponent of Clostridium botulinum type C progenitor toxin
Authors: Nakamura, T. / Kotani, M. / Tonozuka, T. / Ide, A. / Oguma, K. / Nishikawa, A.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

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Assembly

Deposited unit
A: Hemagglutinin components HA-22/23/53
B: Hemagglutinin components HA-22/23/53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6098
Polymers73,3842
Non-polymers1,2246
Water7,188399
1
A: Hemagglutinin components HA-22/23/53
B: Hemagglutinin components HA-22/23/53
hetero molecules

A: Hemagglutinin components HA-22/23/53
B: Hemagglutinin components HA-22/23/53
hetero molecules

A: Hemagglutinin components HA-22/23/53
B: Hemagglutinin components HA-22/23/53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,82624
Polymers220,1536
Non-polymers3,67318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area22380 Å2
ΔGint-67 kcal/mol
Surface area69230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.596, 175.596, 80.779
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Hemagglutinin components HA-22/23/53 / Hemagglutinin components HA70 / HA3


Mass: 26050.873 Da / Num. of mol.: 1 / Fragment: HA22-23(HA3a)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: HA-70 / Plasmid: pMAL-cRI / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P46085
#2: Protein Hemagglutinin components HA-22/23/53 / Hemagglutinin components HA70 / HA3


Mass: 47333.520 Da / Num. of mol.: 1 / Fragment: HA53(HA3b)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: HA-70 / Plasmid: pMAL-cRI / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P46085
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 4.9 Å3/Da / Density % sol: 74.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12%(v/v) 2-methyl-2,4-pentendiol, 20mM CaCl2, 100mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. all: 45881 / Num. obs: 45881 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.7
Reflection shellResolution: 2.56→2.6 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2308 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZS6

2zs6


Resolution: 2.56→25.74 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 111550.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4499 10.1 %RANDOM
Rwork0.188 ---
all0.191 44727 --
obs0.191 44727 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.64 Å2 / ksol: 0.32441 e/Å3
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å24.48 Å20 Å2
2--3.19 Å20 Å2
3----6.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.56→25.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 83 399 5203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.56→2.72 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 756 10.8 %
Rwork0.266 6268 -
obs-7024 92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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