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- PDB-2v9b: X-ray structure of viscotoxin B2 from Viscum album -

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Basic information

Entry
Database: PDB / ID: 2v9b
TitleX-ray structure of viscotoxin B2 from Viscum album
ComponentsVISCOTOXIN-B
KeywordsTOXIN / THIONIN / SECRETED / PLANT TOXIN / PLANT DEFENSE
Function / homology
Function and homology information


defense response / toxin activity / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVISCUM ALBUM (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.05 Å
AuthorsDebreczeni, J.E. / Pal, A. / Kahle, B. / Zeeck, A. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2008
Title: Structures of viscotoxins A1 and B2 from European mistletoe solved using native data alone.
Authors: Pal, A. / Debreczeni, J.E. / Sevvana, M. / Gruene, T. / Kahle, B. / Zeeck, A. / Sheldrick, G.M.
History
DepositionAug 23, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / struct / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _diffrn_source.pdbx_synchrotron_site / _struct.title / _struct_ref_seq_dif.details
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VISCOTOXIN-B
B: VISCOTOXIN-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3078
Polymers9,7312
Non-polymers5766
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-8.9 kcal/mol
Surface area6550 Å2
MethodPQS
Unit cell
Length a, b, c (Å)39.819, 40.392, 44.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (9.0E-6, 0.9913, -0.1315), (0.9827, 0.02427, 0.1837), (0.1853, -0.1292, -0.9742)
Vector: 7.419, -11.22, 5.433)

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Components

#1: Protein/peptide VISCOTOXIN-B / VISCOTOXIN B2


Mass: 4865.536 Da / Num. of mol.: 2 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) VISCUM ALBUM (European mistletoe) / References: UniProt: P08943
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 17 TO ASP ENGINEERED RESIDUE IN CHAIN B, ASN 17 TO ASP
Sequence detailsN11D KNOWN ISOFORM MUTATION

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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: 1.7 Å3/Da / Density % sol: 30 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 1UL HANGING DROP, 30 MG/ML PROTEIN, 0.2M AMSO4, 0.08M CACODYLATE PH 6.5, 25% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.15→20 Å / Num. obs: 34317 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 21.34 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.8
Reflection shellResolution: 1.05→1.15 Å / Redundancy: 21 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 12.6 / % possible all: 99.6

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SADABSdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: NONE

Resolution: 1.05→40 Å / Num. parameters: 7604 / Num. restraintsaints: 10158 / Cross valid method: THROUGHOUT / σ(F): 12 / Stereochemistry target values: ENGH AND HUBER / Details: HYDROGEN ATOMS WERE ADDED IN RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1703 1833 5 %RANDOM
all0.1277 35151 --
obs--99.8 %-
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 646 / Occupancy sum non hydrogen: 795
Refinement stepCycle: LAST / Resolution: 1.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms664 0 30 106 800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0.016
X-RAY DIFFRACTIONs_from_restr_planes0.0285
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.114
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.092

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