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- PDB-2zoe: HA3 subcomponent of Clostridium botulinum type C progenitor toxin... -

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Basic information

Entry
Database: PDB / ID: 2zoe
TitleHA3 subcomponent of Clostridium botulinum type C progenitor toxin, complex with N-acetylneuramic acid
Components(Hemagglutinin components HA3) x 2
KeywordsTOXIN / Hemagglutinin / Jelly roll
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
N-acetyl-beta-neuraminic acid / Hemagglutinin components HA-70 type C
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNakamura, T. / Kotani, M. / Tonozuka, T. / Ide, A. / Oguma, K. / Nishikawa, A.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Sugar-binding sites of the HA1 subcomponent of Clostridium botulinum type C progenitor toxin
Authors: Nakamura, T. / Tonozuka, T. / Ide, A. / Yuzawa, T. / Oguma, K. / Nishikawa, A.
History
DepositionMay 9, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin components HA3
B: Hemagglutinin components HA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7863
Polymers71,4772
Non-polymers3091
Water4,864270
1
A: Hemagglutinin components HA3
B: Hemagglutinin components HA3
hetero molecules

A: Hemagglutinin components HA3
B: Hemagglutinin components HA3
hetero molecules

A: Hemagglutinin components HA3
B: Hemagglutinin components HA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,3589
Polymers214,4306
Non-polymers9283
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area24130 Å2
ΔGint-80 kcal/mol
Surface area70410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.076, 177.076, 81.042
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 HA3 / HA-22-23


Mass: 24002.535 Da / Num. of mol.: 1 / Fragment: HA3a
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: type C / Gene: HA3 / Plasmid: MBP-2xFLAG-HA3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P46085
#2: Protein Hemagglutinin components HA3 / HA-53


Mass: 47474.203 Da / Num. of mol.: 1 / Fragment: HA3b
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: type C / Gene: HA3 / Plasmid: MBP-2xFLAG-HA3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P46085
#3: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.331016 Å3/Da / Density % sol: 76.927475 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 1.2M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 50275 / Num. obs: 44733 / % possible obs: 99.9 % / Biso Wilson estimate: 48.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 41.9
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z5A

2z5a
PDB Unreleased entry


Resolution: 2.6→33.21 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1732201.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4507 10.1 %RANDOM
Rwork0.234 ---
obs0.234 44713 99.9 %-
all-50254 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.2064 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 56.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.88 Å20 Å20 Å2
2--6.88 Å20 Å2
3----13.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.6→33.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 21 270 4997
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 732 9.9 %
Rwork0.294 6655 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top

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