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- PDB-1ntn: THE CRYSTAL STRUCTURE OF NEUROTOXIN-I FROM NAJA NAJA OXIANA AT 1.... -

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Basic information

Entry
Database: PDB / ID: 1ntn
TitleTHE CRYSTAL STRUCTURE OF NEUROTOXIN-I FROM NAJA NAJA OXIANA AT 1.9 ANGSTROMS RESOLUTION
ComponentsNEUROTOXIN I
KeywordsPOSTSYNAPTIC NEUROTOXIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Alpha-elapitoxin-Nno2a
Similarity search - Component
Biological speciesNaja oxiana (Central Asian cobra)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMikhailov, A.M. / Nickitenko, A.V. / Vainshtein, B.K. / Betzel, C. / Wilson, K.
Citation
Journal: Febs Lett. / Year: 1993
Title: Three-dimensional structure of neurotoxin-1 from Naja naja oxiana venom at 1.9 A resolution.
Authors: Nickitenko, A.V. / Michailov, A.M. / Betzel, C. / Wilson, K.S.
#1: Journal: FEBS Lett. / Year: 1993
Title: Three-Dimensional Structure of Neurotoxin-1 from Naja Naja Oxiana Venom at 1.9 Angstroms Resolution
Authors: Nickitenko, A.V. / Mikhailov, A.M. / Betzel, C. / Wilson, K.S.
#2: Journal: Bioorg.Khim. / Year: 1991
Title: Spatial Organization of Backbone of the Neurotoxin-I Molecule from the Naja Naja Oxiana Venom and its Crystal Packing (in Russian)
Authors: Mikhailov, A.M. / Nickitenko, A.V. / Chetverina, E.V. / Trakhanov, S.D. / Vainshtein, B.K.
#3: Journal: FEBS Lett. / Year: 1990
Title: Crystallization and Preliminary X-Ray Diffraction Study of Neurotoxin-I from Naja Naja Oxiana Venom
Authors: Mikhailov, A.M. / Nickitenko, A.V. / Trakhanov, S.D. / Vainshtein, B.K. / Chetverina, E.V.
History
DepositionSep 26, 1994Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEUROTOXIN I


Theoretical massNumber of molelcules
Total (without water)7,9421
Polymers7,9421
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.170, 75.580, 35.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 7
2: RESIDUES 69 - 71 ARE POORLY DEFINED IN THE ELECTRON-DENSITY MAP AND IN REFINEMENT AND MAY BE CORRECTED AT HIGHER RESOLUTION.

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Components

#1: Protein NEUROTOXIN I


Mass: 7942.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja oxiana (Central Asian cobra) / References: UniProt: P01382
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal grow
*PLUS
pH: 4.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein11
20.01 Macetic acid11
350 %iso-propanol12
45 %MPD12
50.01 Macetic acid12pH4.7

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 38 Å / Rmerge(I) obs: 0.044

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→38 Å / σ(F): 1
Details: RESIDUES 69 - 71 ARE POORLY DEFINED IN THE ELECTRON-DENSITY MAP AND IN REFINEMENT
RfactorNum. reflection
obs0.19 4979
Refinement stepCycle: LAST / Resolution: 1.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 0 0 65 599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.014
X-RAY DIFFRACTIONp_angle_d0.030.056
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.062
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.020.018
X-RAY DIFFRACTIONp_chiral_restr0.20.227
X-RAY DIFFRACTIONp_singtor_nbd0.30.214
X-RAY DIFFRACTIONp_multtor_nbd0.30.324
X-RAY DIFFRACTIONp_xhyhbond_nbd0.30.216
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor33.3
X-RAY DIFFRACTIONp_staggered_tor2025.7
X-RAY DIFFRACTIONp_orthonormal_tor2011.5
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 4766 / Rfactor obs: 0.193 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0560.03
X-RAY DIFFRACTIONp_planar_d0.0620.04
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.2270.2

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