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- PDB-3mpp: Botulinum Neurotoxin Type G Receptor Binding Domain -

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Basic information

Entry
Database: PDB / ID: 3mpp
TitleBotulinum Neurotoxin Type G Receptor Binding Domain
ComponentsBotulinum neurotoxin type G
KeywordsTOXIN / beta barrel beta trefoil
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
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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type G
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSchmitt, J.M. / Lacy, D.B.
CitationJournal: Biochemistry / Year: 2010
Title: Structural analysis of botulinum neurotoxin type G receptor binding .
Authors: Schmitt, J. / Karalewitz, A. / Benefield, D.A. / Mushrush, D.J. / Pruitt, R.N. / Spiller, B.W. / Barbieri, J.T. / Lacy, D.B.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Botulinum neurotoxin type G


Theoretical massNumber of molelcules
Total (without water)50,6791
Polymers50,6791
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.630, 90.161, 91.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Botulinum neurotoxin type G / BoNT/G / Bontoxilysin-G / Botulinum neurotoxin G light chain / Botulinum neurotoxin G heavy chain


Mass: 50678.645 Da / Num. of mol.: 1 / Fragment: receptor binding domain (UNP residues 867:1297)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botG / Production host: Escherichia coli (E. coli) / References: UniProt: Q60393, bontoxilysin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12%-15% (w/v) polyethylene glycol 3350, 20 mM Bis-Tris buffer pH 5.75-6.50 and 20-25 mM MgCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 33642 / Num. obs: 33608 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.98→2.03 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EPW

1epw


Resolution: 1.98→40.938 Å / SU ML: 0.09 / σ(F): 1.34 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 1694 5.05 %random
Rwork0.1747 ---
obs0.1771 33548 99.11 %-
all-33849 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.653 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.9735 Å20 Å20 Å2
2--3.2231 Å2-0 Å2
3---2.7503 Å2
Refinement stepCycle: LAST / Resolution: 1.98→40.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 0 332 3660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073458
X-RAY DIFFRACTIONf_angle_d1.074688
X-RAY DIFFRACTIONf_dihedral_angle_d16.2241248
X-RAY DIFFRACTIONf_chiral_restr0.077504
X-RAY DIFFRACTIONf_plane_restr0.004603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.04220.28031270.20162358X-RAY DIFFRACTION90
2.0422-2.10810.23371420.19042620X-RAY DIFFRACTION100
2.1081-2.18340.25591370.18862651X-RAY DIFFRACTION100
2.1834-2.27080.26541320.18182656X-RAY DIFFRACTION100
2.2708-2.37420.24121520.1632625X-RAY DIFFRACTION100
2.3742-2.49930.19861540.16562658X-RAY DIFFRACTION100
2.4993-2.65590.25211330.16382658X-RAY DIFFRACTION100
2.6559-2.86090.23041410.18112668X-RAY DIFFRACTION100
2.8609-3.14870.21181300.16962696X-RAY DIFFRACTION100
3.1487-3.60410.19821460.16392703X-RAY DIFFRACTION100
3.6041-4.53990.17711530.14752717X-RAY DIFFRACTION100
4.5399-40.94640.241470.19332844X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67920.227-0.54122.7087-1.83273.65610.2908-0.13670.20260.65440.25890.598-0.6933-0.3086-0.49790.32090.0270.19560.16720.07350.3484-8.43918.580635.5166
21.60510.4702-0.34011.9184-0.7361.39390.12680.0160.08990.0997-0.0411-0.0084-0.06260.0881-0.07190.0972-0.0047-0.00410.10880.00290.102712.886715.952611.9808
31.1067-0.73560.45360.8223-0.66861.3394-0.02370.050.1706-0.0005-0.0013-0.0838-0.0893-0.02660.02930.1284-0.019-0.02330.12770.01170.18558.170220.95556.6318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain C and resid 1:213)
2X-RAY DIFFRACTION2(chain C and resid 214:367)
3X-RAY DIFFRACTION3(chain C and resid 368:433)

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