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- PDB-4fvv: Crystal structure of HCR/D-Sa-GBL1/C -

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Basic information

Entry
Database: PDB / ID: 4fvv
TitleCrystal structure of HCR/D-Sa-GBL1/C
ComponentsNeurotoxin
KeywordsTOXIN / botulinum toxin / ganglioside bing loop / Ganglioside
Function / homology
Function and homology information


protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Neurotoxin
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFu, Z. / Karalewitz, A. / Baldwin, M.R. / Kim, J.-J.P. / Barbieri, J.T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Botulinum neurotoxin serotype C associates with dual ganglioside receptors to facilitate cell entry.
Authors: Karalewitz, A.P. / Fu, Z. / Baldwin, M.R. / Kim, J.J. / Barbieri, J.T.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 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: Neurotoxin
B: Neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6829
Polymers97,8082
Non-polymers8747
Water3,423190
1
A: Neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2845
Polymers48,9041
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3984
Polymers48,9041
Non-polymers4933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.603, 154.630, 181.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1302-

SO4

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Components

#1: Protein Neurotoxin /


Mass: 48904.074 Da / Num. of mol.: 2 / Fragment: receptor binding domain, UNP residues 862-1285 / Mutation: loop of KLGDDYWFN(1246-1254) mutated to RLGGDWYR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LBR1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLOOP RESIDUES OF KLGDDYWFN(1246-1254) REPLACED BY RLGGDWYR(THE LOOP OF HCRC).

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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: 2.9 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 8.5
Details: 16% PEG5K-MME, 50 mM MgSO4, 0.1 M HEPPs buffer, pH 8.5, EVAPORATION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2011 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→39.38 Å / Num. obs: 31121 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.113 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 3024 / Rsym value: 0.505 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3N7L

3n7l


Resolution: 2.7→39.38 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 52530.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED MISSING RESIDUES THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I='EXPRESSION TAG' CODE.)
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1429 4.9 %RANDOM
Rwork0.206 ---
obs0.206 29067 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.4954 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å20 Å2
2---3.38 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 54 190 6985
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.522.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.421 134 5.2 %
Rwork0.317 2458 -
obs--81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5so4.parso4.top
X-RAY DIFFRACTION6gol.pargol.top
X-RAY DIFFRACTION7slb.parslb.top

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