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- PDB-3v0c: 4.3 angstrom crystal structure of an inactive BoNT/A (E224Q/R363A... -

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Basic information

Entry
Database: PDB / ID: 3v0c
Title4.3 angstrom crystal structure of an inactive BoNT/A (E224Q/R363A/Y366F)
ComponentsBoNT/A
KeywordsTOXIN / Botulinum neurotoxin / Neurotoxin associated protein / Progenitor toxin complex / VHH bound interlocked complex / NTNHA
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / 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 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 ...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
Similarity search - Domain/homology
Botulinum neurotoxin type A / BoNT/A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsGu, S. / Rumpel, S. / Zhou, J. / Strotmeier, J. / Bigalke, H. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Jin, R.
CitationJournal: Science / Year: 2012
Title: Botulinum neurotoxin is shielded by NTNHA in an interlocked complex.
Authors: Gu, S. / Rumpel, S. / Zhou, J. / Strotmeier, J. / Bigalke, H. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Jin, R.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BoNT/A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,2642
Polymers151,1991
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.521, 167.521, 158.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein BoNT/A / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT


Mass: 151198.719 Da / Num. of mol.: 1 / Fragment: Inactive full length BoNT/A1 / Mutation: E224Q,R363A,Y366F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont/a, boNT/A, bonta / Production host: Escherichia coli (E. coli) / References: UniProt: Q7B8V4, UniProt: P0DPI1*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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: 4.25 Å3/Da / Density % sol: 71.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG3350, 200mM MgSO4,100mM Hepes, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2009
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. all: 17896 / Num. obs: 17863 / % possible obs: 100 % / Observed criterion σ(F): 8.4 / Observed criterion σ(I): 8.4
Reflection shellResolution: 4.3→4.4 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BTA

3bta


Resolution: 4.3→45.114 Å / SU ML: 1.68 / σ(F): 1.35 / Phase error: 34.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3492 912 5.11 %RANDOM
Rwork0.3222 ---
all0.3235 17896 --
obs0.3235 17863 99.88 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 195.683 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1474 Å2-0 Å20 Å2
2--7.1474 Å20 Å2
3----14.2947 Å2
Refinement stepCycle: LAST / Resolution: 4.3→45.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10389 0 1 0 10390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02710621
X-RAY DIFFRACTIONf_angle_d1.3814381
X-RAY DIFFRACTIONf_dihedral_angle_d16.2773932
X-RAY DIFFRACTIONf_chiral_restr0.1251585
X-RAY DIFFRACTIONf_plane_restr0.0071852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3003-4.52680.42561280.41022399X-RAY DIFFRACTION100
4.5268-4.81010.38111540.37332354X-RAY DIFFRACTION100
4.8101-5.1810.40611240.34882371X-RAY DIFFRACTION100
5.181-5.70150.40531300.35322409X-RAY DIFFRACTION100
5.7015-6.52440.42951190.3762432X-RAY DIFFRACTION100
6.5244-8.21190.38261330.34132439X-RAY DIFFRACTION100
8.2119-45.11640.25481240.25382547X-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)
12.7937-2.00180.74074.3396-1.7281.0009-0.8862-0.28410.7520.0586-0.13610.2712-1.52990.0971-02.0552-0.2663-0.03791.9431-0.00671.5116-5.801198.31155.4419
21.23021.33341.78863.7361.58191.0951-0.16730.0697-0.1381-0.17690.08810.29750.46280.017301.63790.04650.11521.432-0.06441.3694-5.978180.70189.0404
30.8011-0.73130.68382.55180.06041.62420.3919-0.2339-0.9185-0.64250.3556-0.01440.1855-0.70.00021.4923-0.2840.43961.61850.16441.4147-13.310870.5305-3.3798
42.8823-1.27122.8893.7651-2.6093.63870.11520.04880.1176-0.43440.05450.19880.27720.14440.00161.32760.32390.15821.46720.10311.2024-15.969853.23362.1926
55.93642.74742.39161.82081.19714.1195-0.17551.2943-1.8318-0.78450.6082-1.02390.46881.11520.00441.29730.18930.32031.5244-0.43431.7931-17.795123.87161.6555
63.83272.06143.53826.18330.8191.26740.35-1.11910.83820.9250.17640.18090.8762-0.27260.00011.8267-0.30050.33921.8429-0.11511.9205-50.442217.43970.4374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:80)
2X-RAY DIFFRACTION2chain 'A' and (resseq 81:471)
3X-RAY DIFFRACTION3chain 'A' and (resseq 472:603)
4X-RAY DIFFRACTION4chain 'A' and (resseq 604:859)
5X-RAY DIFFRACTION5chain 'A' and (resseq 860:1112)
6X-RAY DIFFRACTION6chain 'A' and (resseq 1113:1296)

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