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- PDB-1zkx: Crystal structure of Glu158Ala/Thr159Ala/Asn160Ala- a triple muta... -

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Basic information

Entry
Database: PDB / ID: 1zkx
TitleCrystal structure of Glu158Ala/Thr159Ala/Asn160Ala- a triple mutant of Clostridium botulinum neurotoxin E catalytic domain
Componentsbotulinum neurotoxin type E
KeywordsHYDROLASE / botulinum neurotoxin E / catalytic domain / light chain / Glu158Ala/Thr159Ala/Asn160Ala mutant
Function / homology
Function and homology information


Toxicity of botulinum toxin type E (botE) / 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 E (botE) / 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 / extracellular region / zinc ion binding / membrane
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / 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 E
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.52 Å
AuthorsAgarwal, R. / Binz, T. / Swaminathan, S.
CitationJournal: Biochemistry / Year: 2005
Title: Analysis of Active Site Residues of Botulinum Neurotoxin E by Mutational, Functional, and Structural Studies: Glu335Gln Is an Apoenzyme.
Authors: Agarwal, R. / Binz, T. / Swaminathan, S.
History
DepositionMay 4, 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: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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 / _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 1.4Aug 23, 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
A: botulinum neurotoxin type E
B: botulinum neurotoxin type E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3868
Polymers95,1132
Non-polymers2736
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-101 kcal/mol
Surface area34480 Å2
MethodPISA
2
A: botulinum neurotoxin type E
B: botulinum neurotoxin type E
hetero molecules

A: botulinum neurotoxin type E
B: botulinum neurotoxin type E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,77216
Polymers190,2274
Non-polymers54512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7440 Å2
ΔGint-201 kcal/mol
Surface area67220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.904, 144.784, 83.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein botulinum neurotoxin type E


Mass: 47556.699 Da / Num. of mol.: 2 / Fragment: catalytic domain (residues 2-421) / Mutation: E158A/T159A/N160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: NCTC-11219 / Plasmid: PET-9C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q00496, bontoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.67 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Ammonium sulfate, lithium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2004 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 36986 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.4
Reflection shellHighest resolution: 2.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / Num. unique all: 1986 / % possible all: 54.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1T3A

1t3a


Resolution: 2.52→46.5 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 140865.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
Details: In general, three loop regions (50-65, 188-200 and 234-244) are either disordered or have very weak electron density in both chains. In this entry, the missing residues are due to the ...Details: In general, three loop regions (50-65, 188-200 and 234-244) are either disordered or have very weak electron density in both chains. In this entry, the missing residues are due to the absence of interpretable electron density in those regions.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 812 3 %RANDOM
Rwork0.208 ---
obs-26891 72.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.7707 Å2 / ksol: 0.322355 e/Å3
Displacement parametersBiso mean: 38.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.95 Å20 Å20 Å2
2---10.82 Å20 Å2
3---6.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.52→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6299 0 6 243 6548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.2
LS refinement shellResolution: 2.52→2.68 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 61 3 %
Rwork0.301 1983 -
obs--33.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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