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- PDB-2h8u: Bucain, a cardiotoxin from the Malayan Krait Bungarus candidus -

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Basic information

Entry
Database: PDB / ID: 2h8u
TitleBucain, a cardiotoxin from the Malayan Krait Bungarus candidus
ComponentsBucain
KeywordsTOXIN / bucain / cardiotoxin
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesBungarus candidus (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMurakami, M.T. / Kini, R.M. / Arni, R.K.
CitationJournal: To be Published
Title: Crystal Structure of Bucain
Authors: Murakami, M.T. / Kini, R.M. / Arni, R.K.
History
DepositionJun 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bucain
B: Bucain


Theoretical massNumber of molelcules
Total (without water)14,4572
Polymers14,4572
Non-polymers00
Water1,51384
1
A: Bucain


Theoretical massNumber of molelcules
Total (without water)7,2291
Polymers7,2291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bucain


Theoretical massNumber of molelcules
Total (without water)7,2291
Polymers7,2291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.617, 62.888, 78.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assemby is a monomer from the dimer in the asymmetric unit.

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Components

#1: Protein Bucain


Mass: 7228.554 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bungarus candidus (cobra) / References: UniProt: P83346
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / pH: 5.6
Details: peg 4000, ammonium acetate, pH 5.6, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.51 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51 Å / Relative weight: 1
ReflectionResolution: 2.1→17.2 Å / Num. all: 7680 / Num. obs: 7426 / % possible obs: 74.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5
Reflection shellResolution: 2.1→2.16 Å / % possible all: 72.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→17.2 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.445 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.303 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26575 354 4.8 %RANDOM
Rwork0.20378 ---
all0.216 7426 --
obs0.20668 7072 74.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--3.18 Å20 Å2
3----2.94 Å2
Refinement stepCycle: LAST / Resolution: 2.1→17.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 0 84 1088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221029
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9831385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6835130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5812635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.98915212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.368154
X-RAY DIFFRACTIONr_chiral_restr0.1340.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02732
X-RAY DIFFRACTIONr_nbd_refined0.2460.2370
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.24
X-RAY DIFFRACTIONr_mcbond_it1.2681.5669
X-RAY DIFFRACTIONr_mcangle_it2.21421052
X-RAY DIFFRACTIONr_scbond_it3.1113418
X-RAY DIFFRACTIONr_scangle_it4.9664.5332
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 25 -
Rwork0.225 339 -
obs--50.35 %

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