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- PDB-1zb7: Crystal Structure of Botulinum Neurotoxin Type G Light Chain -

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Basic information

Entry
Database: PDB / ID: 1zb7
TitleCrystal Structure of Botulinum Neurotoxin Type G Light Chain
Componentsneurotoxin
KeywordsTOXIN / HExxH metalloprotease
Function / homology
Function and homology information


Toxicity of botulinum toxin type G (botG) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...Toxicity of botulinum toxin type G (botG) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
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 C-terminal / Clostridium neurotoxin, receptor binding N-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 C-terminal / Clostridium neurotoxin, receptor binding N-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
CITRATE ANION / Botulinum neurotoxin type G
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsArndt, J.W. / Yu, W. / Bi, F. / Stevens, R.C.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structure of botulinum neurotoxin type g light chain: serotype divergence in substrate recognition
Authors: Arndt, J.W. / Yu, W. / Bi, F. / Stevens, R.C.
History
DepositionApr 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1973
Polymers51,9431
Non-polymers2552
Water3,549197
1
A: neurotoxin
hetero molecules

A: neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3956
Polymers103,8862
Non-polymers5094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area5020 Å2
ΔGint-104 kcal/mol
Surface area34730 Å2
MethodPISA, PQS
2
A: neurotoxin
hetero molecules

A: neurotoxin
hetero molecules

A: neurotoxin
hetero molecules

A: neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,78912
Polymers207,7714
Non-polymers1,0188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Buried area13890 Å2
ΔGint-225 kcal/mol
Surface area65610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.8660, 178.8660, 80.8640
Angle α, β, γ (deg.)90, 90, 120
Int Tables number180
Space group name H-MP6222
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations:

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Components

#1: Protein neurotoxin


Mass: 51942.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Plasmid: pBN13 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q60393
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.5 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 6.00% PEG 6000, 0.65M Lithium Chloride, 0.10M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.00863 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00863 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 30233 / Num. obs: 30233 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rsym value: 0.053 / Net I/σ(I): 24.4
Reflection shellResolution: 2.35→2.411 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.395 / % possible all: 95.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0011refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F82

1f82


Resolution: 2.35→24.81 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.871 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22216 1536 5.1 %RANDOM
Rwork0.17364 ---
all0.17612 28690 --
obs0.17364 28690 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å20 Å2
2--0.09 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.35→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 14 197 3533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223417
X-RAY DIFFRACTIONr_bond_other_d0.0060.023008
X-RAY DIFFRACTIONr_angle_refined_deg2.0311.9664625
X-RAY DIFFRACTIONr_angle_other_deg1.04637055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7825410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96625.091165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41415587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8631512
X-RAY DIFFRACTIONr_chiral_restr0.1320.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023771
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02672
X-RAY DIFFRACTIONr_nbd_refined0.2140.2646
X-RAY DIFFRACTIONr_nbd_other0.2030.22962
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21637
X-RAY DIFFRACTIONr_nbtor_other0.0960.21887
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2183
X-RAY DIFFRACTIONr_metal_ion_refined0.230.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3750.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.212
X-RAY DIFFRACTIONr_mcbond_it1.8311.52155
X-RAY DIFFRACTIONr_mcbond_other0.31.5829
X-RAY DIFFRACTIONr_mcangle_it2.28323364
X-RAY DIFFRACTIONr_scbond_it3.58831473
X-RAY DIFFRACTIONr_scangle_it5.2534.51261
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 115 -
Rwork0.233 2093 -
obs--95.3 %

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