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- PDB-1okh: Viscotoxin A3 from Viscum album L. -

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Basic information

Entry
Database: PDB / ID: 1okh
TitleViscotoxin A3 from Viscum album L.
ComponentsVISCOTOXIN A3
KeywordsTOXIN / THIONIN / 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
PHOSPHATE ION / Viscotoxin-A3
Similarity search - Component
Biological speciesVISCUM ALBUM (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsDebreczeni, J.E. / Girmann, B. / Zeeck, A. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of Viscotoxin A3: Disulfide Location from Weak Sad Data
Authors: Debreczeni, J.E. / Girmann, B. / Zeeck, A. / Kratzner, R. / Sheldrick, G.M.
History
DepositionJul 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2003Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VISCOTOXIN A3
B: VISCOTOXIN A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9715
Polymers9,6852
Non-polymers2863
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.995, 68.593, 25.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

21B-2004-

HOH

31B-2005-

HOH

41B-2006-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.19986, -0.97837, -0.05339), (-0.97982, -0.19943, -0.01338), (0.00245, 0.05499, -0.99848)
Vector: -0.01244, 0.50519, 30.12263)

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Components

#1: Protein/peptide VISCOTOXIN A3


Mass: 4842.626 Da / Num. of mol.: 2 / Fragment: VISCOTOXIN A3 CHAIN, RESIDUES 27-72 / Source method: isolated from a natural source / Source: (natural) VISCUM ALBUM (European mistletoe) / Organ: LEAVES, STEMS / References: UniProt: P01538
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.79 Å3/Da / Density % sol: 31.5 %
Description: DATA COLLECTED IN-HOUSE. PHASED USING IN-HOUSE SULFUR- SAD DATA
Crystal growpH: 6.5
Details: 0.15M AM2SO4, 0.05M CACOD. PH=6.5, 30% PEG8000, 15MM HGCL2, pH 6.50
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
20.15 Mammonium sulfate1reservoir
30.05 Mcacodylate1reservoirpH6.5
430 %PEG80001reservoir
515 mM1reservoirHgCl2

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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: IMAGE PLATE / Date: Apr 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→68.59 Å / Num. obs: 8938 / % possible obs: 100 % / Redundancy: 5.25 % / Rmerge(I) obs: 0.0892 / Net I/σ(I): 14.31
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.42 % / Rmerge(I) obs: 0.3866 / Mean I/σ(I) obs: 3.89 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 1.75 Å / Redundancy: 5.3 % / Num. measured all: 50787 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.75→20 Å / Num. parameters: 3115 / Num. restraintsaints: 2935 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.257 454 5.1 %RANDOM
all0.192 8893 --
obs0.1887 -100 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 780
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms666 0 15 94 775
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.002
X-RAY DIFFRACTIONs_from_restr_planes0.293
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.239 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.293
X-RAY DIFFRACTIONs_chiral_restr0.029

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