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- PDB-1djt: ATOMIC RESOLUTION STRUCTURE OF SCORPION ALPHA-LIKE TOXIN BMK M1 I... -

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Basic information

Entry
Database: PDB / ID: 1djt
TitleATOMIC RESOLUTION STRUCTURE OF SCORPION ALPHA-LIKE TOXIN BMK M1 IN A NEW CRYSTAL FORM
ComponentsALPHA-LIKE NEUROTOXIN BMK M1
KeywordsTOXIN / SCORPION / ALPHA-LIKE NEUROTOXIN / NON-PROLINE CIS PEPTIDE BOND / ATOMIC RESOLUTION
Function / homology
Function and homology information


sodium channel inhibitor activity / defense response / toxin activity / extracellular region
Similarity search - Function
LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like ...LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain / Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-like toxin BmK M1
Similarity search - Component
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsWang, D.-C. / He, X.-L.
Citation
Journal: To be Published
Title: Atomic Resolution Structure of Scorpion Alpha-Like Toxin BmK M1 in a New Crystal Form
Authors: Wang, D.-C. / He, X.-L.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structures of Two Scorpion Alpha-Like Toxins: Non-Proline Cis Peptide Bonds and Implications for New Binding Site Selectivity on the Sodium Channel
Authors: He, X.-L. / Li, H.-M. / Zeng, Z.-H. / Li, X.-Q. / Wang, M. / Wang, D.-C.
History
DepositionDec 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-LIKE NEUROTOXIN BMK M1
B: ALPHA-LIKE NEUROTOXIN BMK M1


Theoretical massNumber of molelcules
Total (without water)14,4712
Polymers14,4712
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.120, 52.770, 76.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer related by a 2-fold non-crystallographic axis

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Components

#1: Protein ALPHA-LIKE NEUROTOXIN BMK M1


Mass: 7235.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: KARSCH SCORPION / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Organ: TAIL GLAND / References: UniProt: P45697
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 1.89 Å3/Da / Density % sol: 34.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.8M NAH2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 15, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 56850 / Num. obs: 25220 / % possible obs: 70.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.2→1.23 Å / % possible all: 35

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
RefinementResolution: 1.2→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection
all0.109 25220
obs0.109 25220
Rfree-2530
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 192 1213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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