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- PDB-2fpq: Crystal Structure of Botulinum Neurotoxin Type D Light Chain -

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Basic information

Entry
Database: PDB / ID: 2fpq
TitleCrystal Structure of Botulinum Neurotoxin Type D Light Chain
ComponentsBOTULINUM NEUROTOXIN D LIGHT CHAIN
KeywordsTOXIN / HEXXH METALLOPROTEASE
Function / homology
Function and homology information


Toxicity of botulinum toxin type D (botD) / ganglioside GT1b binding / bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Botulinum neurotoxin type D
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsArndt, J.W. / Chai, Q. / Christian, T. / Stevens, R.C.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of Botulinum Neurotoxin Type D Light Chain at 1.65 A Resolution: Repercussions for VAMP-2 Substrate Specificity(,).
Authors: Arndt, J.W. / Chai, Q. / Christian, T. / Stevens, R.C.
History
DepositionJan 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: BOTULINUM NEUROTOXIN D LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7613
Polymers50,6571
Non-polymers1052
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.829, 89.818, 54.400
Angle α, β, γ (deg.)90.00, 94.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BOTULINUM NEUROTOXIN D LIGHT CHAIN


Mass: 50656.965 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: D16PHI / Gene: BOTD / Production host: Escherichia coli (E. coli) / References: UniProt: P19321, bontoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% PEG 4000, 200MM POTASSIUM THIOCYANATE, 100MM SODIUM ACETATE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00863
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2005
RadiationMonochromator: KOHZU: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00863 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 53579 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 35.2 Å2 / Rsym value: 0.049 / Net I/σ(I): 21.6
Reflection shellResolution: 1.65→1.69 Å / % possible all: 90.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0003refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.137 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2594 5.1 %RANDOM
Rwork0.182 ---
obs0.184 48292 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.2 Å2
2---0.34 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 2 375 3708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223492
X-RAY DIFFRACTIONr_bond_other_d0.0060.023073
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.9554748
X-RAY DIFFRACTIONr_angle_other_deg0.89537189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.0045428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51124.551167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29615587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3091516
X-RAY DIFFRACTIONr_chiral_restr0.1140.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023872
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02716
X-RAY DIFFRACTIONr_nbd_refined0.2270.2748
X-RAY DIFFRACTIONr_nbd_other0.1970.23180
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21748
X-RAY DIFFRACTIONr_nbtor_other0.0880.21831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9891.52118
X-RAY DIFFRACTIONr_mcbond_other0.3121.5843
X-RAY DIFFRACTIONr_mcangle_it1.63323467
X-RAY DIFFRACTIONr_scbond_it2.64731394
X-RAY DIFFRACTIONr_scangle_it4.0134.51276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 176 -
Rwork0.264 3442 -
obs--90.84 %

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