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- PDB-1qxm: Crystal structure of a hemagglutinin component (HA1) from type C ... -

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Basic information

Entry
Database: PDB / ID: 1qxm
TitleCrystal structure of a hemagglutinin component (HA1) from type C Clostridium botulinum
ComponentsHA1
KeywordsTOXIN / Clostridium botulinum / hemagglutinin / HA1 / trefoil
Function / homology
Function and homology information


carbohydrate binding / extracellular region
Similarity search - Function
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
Main hemagglutinin component type D / Main hemagglutinin component type C
Similarity search - Component
Biological speciesClostridium botulinum D phage (virus)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.7 Å
AuthorsInoue, K. / Sobhany, M. / Transue, T.R. / Oguma, K. / Pedersen, L.C. / Negishi, M.
CitationJournal: Microbiology / Year: 2003
Title: Structural analysis by X-ray crystallography and calorimetry of a haemagglutinin component (HA1) of the progenitor toxin from Clostridium botulinum.
Authors: Inoue, K. / Sobhany, M. / Transue, T.R. / Oguma, K. / Pedersen, L.C. / Negishi, M.
History
DepositionSep 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HA1
B: HA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5339
Polymers71,0992
Non-polymers4347
Water11,728651
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.173, 62.332, 82.321
Angle α, β, γ (deg.)90.00, 104.53, 90.00
Int Tables number5
Space group name H-MC121
Detailsnot known

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Components

#1: Protein HA1


Mass: 35549.348 Da / Num. of mol.: 2 / Fragment: hemagglutinin component HA1 / Mutation: type C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum D phage (virus) / Species: Clostridium phage c-st / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P46084, UniProt: P0DPR1*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 296 K / Method: sirsas / pH: 5.5
Details: MES, PEG8000, MgCl2, pH 5.5, SIRSAS, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMMES1droppH5.5
225 mg/mlprotein1drop
30.1 MMES1reservoirpH5.5
4100 mM1reservoirMgCl2
510 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 71843 / Num. obs: 71843 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.042 / Net I/σ(I): 23.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2 % / Mean I/σ(I) obs: 8 / Num. unique all: 6546 / Rsym value: 0.15 / % possible all: 87.6
Reflection
*PLUS
Num. measured all: 203352 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 87.6 % / Rmerge(I) obs: 0.15

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→24.58 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3610 5.1 %RANDOM
Rwork0.177 ---
all0.178 74815 --
obs0.177 71205 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5967 Å2 / ksol: 0.361759 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.51 Å2
2---0.63 Å20 Å2
3---1.08 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4744 0 28 651 5423
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.542
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 556 5.3 %
Rwork0.222 9985 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2EDO.PAR
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67

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