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- PDB-1sn4: STRUCTURE OF SCORPION NEUROTOXIN BMK M4 -

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Basic information

Entry
Database: PDB / ID: 1sn4
TitleSTRUCTURE OF SCORPION NEUROTOXIN BMK M4
ComponentsPROTEIN (NEUROTOXIN BMK M4)
KeywordsTOXIN / NEUROTOXIN / SODIUM CHANNEL INHIBITOR / SCORPION
Function / homologyScorpion long chain toxin/defensin / Knottin, scorpion toxin-like / Scorpion long chain toxin / Knottin, scorpion toxin-like superfamily / Scorpion toxin-like domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / ion channel inhibitor activity / defense response / toxin activity / extracellular region ...Scorpion long chain toxin/defensin / Knottin, scorpion toxin-like / Scorpion long chain toxin / Knottin, scorpion toxin-like superfamily / Scorpion toxin-like domain / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / ion channel inhibitor activity / defense response / toxin activity / extracellular region / Neurotoxin BmK-M9 / Alpha-like toxin BmK-M4
Function and homology information
Specimen sourceMesobuthus martensii (Chinese scorpion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.3 Å resolution
AuthorsHe, X.L. / Li, H.M. / Liu, X.Q. / Zeng, Z.H. / Wang, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structures of two alpha-like scorpion 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. / Liu, X.Q. / Wang, M. / Wang, D.C.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structure of Toxin II from the Scorpion Androctonus Australis Hector Refined at 1.3 A Resolution
Authors: Housset, D. / Habersetzer-Rochat, C. / Astier, J.P. / Fontecilla-Camps, J.C.
#2: Journal: Zool.Res.Sinica. / Year: 1989
Title: Purification and Partial Characterization of Several New Neurotoxins from East_ Asia Scorpion Crystallographic Studies on an Acidic Toxin from Scorpion Buthus Martensii Karsch
Authors: Hu, R.Q. / Wang, M. / LIU, J.N. / LEI, K.J.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Structure of Scorpion Toxin Variant-3 at 1.2 A Resolution
Authors: Zhao, B. / Carson, M. / Ealick, S.E. / Bugg, C.E.
#4: Journal: Toxicon / Year: 1997
Title: Purification and Sequence Determination of a New Neutral Mammalian Neurotoxin from the Scorpion Buthus Martensii Karsch
Authors: Luo, M.J. / Xiong, Y.M. / Wang, M. / Wang, D.C. / Chi, C.W.
#5: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structure of an Acidic Neurotoxin from Scorpion Buthus Martensii Karsch at 1.85A Resolution
Authors: Li, H.M. / Wang, D.C. / Jin, L. / ZENG, Z.H. / Hu, R.Q.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 11, 1998 / Release: Nov 17, 1999
RevisionDateData content typeGroupCategoryProviderType
1.0Nov 17, 1999Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (NEUROTOXIN BMK M4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3256
Polyers7,0301
Non-polymers2955
Water2,108117
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)54.880, 54.880, 33.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP 61

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Components

#1: Protein/peptide PROTEIN (NEUROTOXIN BMK M4) / BMK-IV


Mass: 7029.957 Da / Num. of mol.: 1 / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Genus: Mesobuthus / Organ: TAIL / Secretion: VENOM / References: UniProt: P45698, UniProt: P58328*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Formula: C2H3O2 / Acetate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Formula: H2O / Water

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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: 2.07 / Density percent sol: 40.6 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temp: 23 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
120 mg/mlprotein1drop
20.001 Macetic acid1drop
34.8 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 283 kelvins
SourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Collection date: Dec 14, 1991
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 20.2 Å2 / D resolution high: 1.3 Å / D resolution low: 21.3 Å / Number obs: 10577 / Rmerge I obs: 0.062 / NetI over sigmaI: 3.7 / Redundancy: 2.2 % / Percent possible obs: 73.5
Reflection shellRmerge I obs: 0.32 / Highest resolution: 1.3 Å / Lowest resolution: 1.35 Å / MeanI over sigI obs: 2.2 / Redundancy: 1.8 % / Percent possible all: 51.2
Reflection
*PLUS
Number obs: 10578 / Number measured all: 23268
Reflection shell
*PLUS
Percent possible obs: 60.2

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Processing

Software
NameClassification
WEISdata scaling
WEISdata reduction
AMoREphasing
X-PLORrefinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BMK M1

R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 26.9 Å2
Least-squares processR factor R free: 0.192 / R factor R work: 0.166 / R factor obs: 0.166 / Highest resolution: 1.3 Å / Lowest resolution: 2 Å / Number reflection R free: 998 / Number reflection obs: 10577 / Percent reflection R free: 10 / Percent reflection obs: 73.5
Refine hist #LASTHighest resolution: 1.3 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 492 / Nucleic acid: 0 / Ligand: 20 / Solvent: 117 / Total: 629
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.732
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.38
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.065
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS shellHighest resolution: 1.3 Å / R factor R free: 0.343 / R factor R work: 0.299 / Lowest resolution: 1.35 Å / Number reflection R free: 72 / Number reflection R work: 662 / Total number of bins used: 10 / Percent reflection R free: 10.8 / Percent reflection obs: 51.2
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine
*PLUS
Sigma F: 2
Displacement parameters
*PLUS
B iso mean: 26.9 Å2
Least-squares process
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 2 Å / Percent reflection R free: 1
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.38
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.065
Refine LS shell
*PLUS
Percent reflection R free: 10.8 / R factor R free: 0.343 / R factor R work: 0.299

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