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- PDB-1vcy: VVA2 isoform -

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Basic information

Entry
Database: PDB / ID: 1vcy
TitleVVA2 isoform
Componentsvolvatoxin A2
KeywordsTOXIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Delta-endotoxin CytB / Delta-endotoxin CytB-like / Delta-endotoxin CytB / Delta-endotoxin CytB-like superfamily / Bacillus thuringiensis toxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Volvatoxin A2
Similarity search - Component
Biological speciesVolvariella volvacea (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLin, S.-C. / Lo, Y.-C. / Lin, J.-Y. / Liaw, Y.-C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structures and electron micrographs of fungal volvatoxin A2
Authors: Lin, S.-C. / Lo, Y.-C. / Lin, J.-Y. / Liaw, Y.-C.
History
DepositionMar 17, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4796
Polymers23,9691
Non-polymers5105
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.107, 56.107, 132.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein volvatoxin A2


Mass: 23968.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: isoform / Source: (natural) Volvariella volvacea (fungus) / References: UniProt: Q6USC4
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.32 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, PEGMME 5000, malonic acid, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→29.51 Å / Num. all: 7054 / Num. obs: 7022 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 64.2 Å2 / Limit h max: 22 / Limit h min: 0 / Limit k max: 15 / Limit k min: 0 / Limit l max: 52 / Limit l min: 0 / Observed criterion F max: 485786.83 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.1
Reflection shellResolution: 2.6→2.72 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1refinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PP0

1pp0


Resolution: 2.6→29.51 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 737 11 %random
Rwork0.225 ---
all-7040 --
obs-6728 95.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 48.7833 Å2 / ksol: 0.360384 e/Å3
Displacement parametersBiso max: 105.37 Å2 / Biso mean: 60.38 Å2 / Biso min: 23.32 Å2
Baniso -1Baniso -2Baniso -3
1-8.77 Å20 Å20 Å2
2--8.77 Å20 Å2
3----17.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.45 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 35 17 1602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.720.488710.20.3796770.0485776489.1
2.72-2.860.3838710.30.3466930.03684678092.2
2.86-3.040.344799.20.327280.03685680794.3
3.04-3.280.329010.40.2627370.02886282795.9
3.28-3.60.2749210.50.2067580.02287385097.4
3.6-4.120.2789310.60.2067680.02287586198.3
4.12-5.190.22710011.10.1777880.01890088898.7
5.19-29.510.23910911.10.2178420.02197895197.2

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