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- PDB-3c8p: X-ray structure of Viscotoxin A1 from Viscum album L. -

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Basic information

Entry
Database: PDB / ID: 3c8p
TitleX-ray structure of Viscotoxin A1 from Viscum album L.
ComponentsViscotoxin A1
KeywordsTOXIN / helix turn helix
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 / SAD / Resolution: 1.25 Å
AuthorsPal, A. / Debreczeni, J.E. / Sevvana, M. / Gruene, T. / Kahle, B. / Zeeck, A. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / 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
DepositionFeb 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Viscotoxin A1
B: Viscotoxin A1


Theoretical massNumber of molelcules
Total (without water)9,7932
Polymers9,7932
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.730, 65.730, 47.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-3127-

HOH

21A-3135-

HOH

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Components

#1: Protein/peptide Viscotoxin A1


Mass: 4896.630 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: D0VWT3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 1.4M Sodium citrate, 0.1 M HEPES pH 7.5, vapor diffusion, temperature 298K, pH 7.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODEBRUKER AXS MICROSTAR11.54
SYNCHROTRONEMBL/DESY, HAMBURG BW7B21
Detector
TypeIDDetectorDateDetails
BRUKER SMART 60001CCDOct 10, 2004OSMIC FOCUSSING MIRRORS
MAR scanner 345 mm plate2IMAGE PLATEFeb 8, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CU K A CRYSTAL MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2Silicon Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
211
ReflectionResolution: 1.25→47.16 Å / Num. obs: 29217 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.0891 / Rsym value: 0.031 / Net I/σ(I): 25.5
Reflection shellResolution: 1.25→1.35 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.3038 / Mean I/σ(I) obs: 2.61 / Rsym value: 0.3038 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.004data extraction
SAINTdata reduction
SADABSdata scaling
XPREPdata reduction
SHELXDphasing
SHELXEmodel building
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.25→47.16 Å / Num. parameters: 7269 / Num. restraintsaints: 8599 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1445 4.95 %RANDOM
all0.1498 29166 --
obs0.151 -100 %-
Solvent computationSolvent model: MEWS AND KRETSINGER
Displacement parametersBiso mean: 17.81 Å2
Refine analyzeNum. disordered residues: 1 / Occupancy sum non hydrogen: 801.79
Refinement stepCycle: LAST / Resolution: 1.25→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms674 0 0 135 809
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.36
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.108

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