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- PDB-3nds: Crystal structure of engineered Naja Nigricollis toxin alpha -

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Basic information

Entry
Database: PDB / ID: 3nds
TitleCrystal structure of engineered Naja Nigricollis toxin alpha
ComponentsShort neurotoxin 1
KeywordsTOXIN / Disulfide pairing / folding intermediates / Three finger toxin fold / Snake toxin / venom
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsStura, E.A. / Drevet, P. / Gregory, G. / Gallopin, M. / Vandame, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Conformational exchange is critical for the productivity of an oxidative folding intermediate with buried free cysteines.
Authors: Gross, G. / Gallopin, M. / Vandame, M. / Couprie, J. / Stura, E. / Zinn-Justin, S. / Drevet, P.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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: Short neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3435
Polymers6,8931
Non-polymers4514
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.666, 40.666, 72.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Short neurotoxin 1 / Neurotoxin alpha


Mass: 6892.859 Da / Num. of mol.: 1 / Fragment: ENGINEERED TOXIN ALPHA / Mutation: inserted Ser 18 / Source method: obtained synthetically
Details: This sequence has ser18 inserted in the alpha toxin from Naja nigricollis.
References: UniProt: P01426
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25 mg/ml toxin alpha-62 mutant lyophilized (2mg resuspende in 80 l 50mM sodium acetate, pH 4.25, 0.02% NaN3. precipitant: 1.8M A.S., 5% MPD, 80mM Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794913 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2006 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794913 Å / Relative weight: 1
ReflectionResolution: 1.2→40.83 Å / Num. all: 19632 / Num. obs: 19396 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 13.3 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.07 / Net I/σ(I): 28.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.2-1.268.40.6463.325920.64693.9
1.26-1.3413.30.4885.926430.48899.5
1.34-1.4314.80.3221024860.32299.7
1.43-1.5514.80.1916.924860.1999.8
1.55-1.714.70.11327.921830.113100
1.7-1.914.60.07639.119670.076100
1.9-2.1914.30.0655417690.065100
2.19-2.6813.80.05761.315210.057100
2.68-3.7912.90.03669.512030.03699.8
3.79-40.8311.40.03567.86930.03594.7

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IQ9

1iq9


Resolution: 1.2→28.755 Å / SU ML: 0.06 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 991 5.12 %RANDOM
Rwork0.1704 ---
obs0.1718 19346 98.51 %-
all-19632 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.895 Å2 / ksol: 0.426 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5977 Å20 Å2-0 Å2
2--0.5977 Å20 Å2
3----1.1954 Å2
Refinement stepCycle: LAST / Resolution: 1.2→28.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms475 0 29 96 600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014763
X-RAY DIFFRACTIONf_angle_d2.4991031
X-RAY DIFFRACTIONf_dihedral_angle_d19.987296
X-RAY DIFFRACTIONf_chiral_restr0.205110
X-RAY DIFFRACTIONf_plane_restr0.012137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.2-1.26330.24281280.18712409253793
1.2633-1.34250.16431410.1532576271799
1.3425-1.44610.14231460.130126062752100
1.4461-1.59160.15071280.120826342762100
1.5916-1.82190.15181680.126126172785100
1.8219-2.29530.18081430.134526982841100
2.2953-28.76370.22811370.19122815296298

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