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- PDB-1uos: The Crystal Structure of the Snake Venom Toxin Convulxin -

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Basic information

Entry
Database: PDB / ID: 1uos
TitleThe Crystal Structure of the Snake Venom Toxin Convulxin
Components
  • CONVULXIN ALPHA
  • CONVULXIN BETA
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / LECTIN / CONVULXIN / C-TYPE LECTIN / SNAKE TOXIN / GPVI / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Snaclec convulxin subunit alpha / Snaclec convulxin subunit beta
Similarity search - Component
Biological speciesCROTALUS DURISSUS TERRIFICUS (tropical rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBatuwangala, T. / Leduc, M. / Gibbins, J.M. / Bon, C. / Jones, E.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the Snake-Venom Toxin Convulxin
Authors: Batuwangala, T. / Leduc, M. / Gibbins, J.M. / Bon, C. / Jones, E.Y.
History
DepositionSep 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CONVULXIN ALPHA
B: CONVULXIN BETA
C: CONVULXIN ALPHA
D: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)61,5554
Polymers61,5554
Non-polymers00
Water5,765320
1
A: CONVULXIN ALPHA
B: CONVULXIN BETA

A: CONVULXIN ALPHA
B: CONVULXIN BETA

A: CONVULXIN ALPHA
B: CONVULXIN BETA

A: CONVULXIN ALPHA
B: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)123,1118
Polymers123,1118
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
2
C: CONVULXIN ALPHA
D: CONVULXIN BETA

C: CONVULXIN ALPHA
D: CONVULXIN BETA

C: CONVULXIN ALPHA
D: CONVULXIN BETA

C: CONVULXIN ALPHA
D: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)123,1118
Polymers123,1118
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
3
A: CONVULXIN ALPHA
B: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)30,7782
Polymers30,7782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-23.74 kcal/mol
Surface area12980 Å2
MethodPISA
4
C: CONVULXIN ALPHA
D: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)30,7782
Polymers30,7782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-23.96 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.458, 132.458, 112.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.44611, 0.89498, -0.00226), (0.89498, -0.44611, 0.00215), (0.00092, -0.00298, -1)0.06458, -0.28705, 11.3536
2given(0.44611, 0.89498, -0.00226), (0.89498, -0.44611, 0.00215), (0.00092, -0.00298, -1)0.06458, -0.28705, 11.3536
DetailsTHE STRUCTURE OF THE CVX IS DESCRIBED AS AN(ALPHA-BETA)X4 TETRAMERIC STRUCTURE.

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Components

#1: Protein CONVULXIN ALPHA / CVX ALPHA


Mass: 15745.936 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) CROTALUS DURISSUS TERRIFICUS (tropical rattlesnake)
References: UniProt: O93426
#2: Protein CONVULXIN BETA / CVX BETA


Mass: 15031.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) CROTALUS DURISSUS TERRIFICUS (tropical rattlesnake)
References: UniProt: O93427
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 4.02 Å3/Da / Density % sol: 71 %
Crystal growpH: 4 / Details: 100MM NA-ACETATE PH 4.0, 25% 1,4-BUTANEDIOL
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
310 mM1dropNaCl
4100 mMsodium acetate1reservoirpH4.0
520-30 %1,4-butanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.01
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2002 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 27008 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.205 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Num. measured all: 154959 / Rmerge(I) obs: 0.205
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJ3

1bj3


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1876353.51 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 908 3.4 %RANDOM
Rwork0.235 ---
obs0.235 26745 99.8 %-
Displacement parametersBiso mean: 60.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.56 Å20 Å20 Å2
2--4.56 Å20 Å2
3----9.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 0 320 4608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.931.5
X-RAY DIFFRACTIONc_mcangle_it5.822
X-RAY DIFFRACTIONc_scbond_it7.042
X-RAY DIFFRACTIONc_scangle_it8.812.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 135 3 %
Rwork0.355 4293 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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