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- PDB-1vgf: volvatoxin A2 (diamond crystal form) -

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Basic information

Entry
Database: PDB / ID: 1vgf
Titlevolvatoxin A2 (diamond crystal form)
Componentsvolvatoxin A2
KeywordsTOXIN / pore formation / fungus / cardiotoxin
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
ACETATE ION / Volvatoxin A2
Similarity search - Component
Biological speciesVolvariella volvacea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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
DepositionApr 24, 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1279
Polymers44,7142
Non-polymers4137
Water61334
1
A: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5344
Polymers22,3571
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5935
Polymers22,3571
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.310, 56.310, 264.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-26-

HOH

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Components

#1: Protein volvatoxin A2


Mass: 22356.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Volvariella volvacea (fungus) / References: UniProt: Q6USC4
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.35 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate, PEG 4000, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.92040, 0.9201, 0.9199, 0.9070
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92041
20.92011
30.91991
40.9071
ReflectionResolution: 2.6→28.54 Å / Num. all: 14033 / Num. obs: 14033 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Redundancy: 34.87 % / Biso Wilson estimate: 45.2 Å2 / Limit h max: 21 / Limit h min: 0 / Limit k max: 15 / Limit k min: 0 / Limit l max: 101 / Limit l min: 0 / Observed criterion F max: 379812.15 / Observed criterion F min: 0.63 / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 10.33 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNS1refinement
ADSC(QUANTUM)data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→28.54 Å / Rfactor Rfree error: 0.007 / 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
Rfree0.268 1371 9.8 %random
Rwork0.214 ---
all-14057 --
obs-13948 99.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 42.5819 Å2 / ksol: 0.359656 e/Å3
Displacement parametersBiso max: 92.99 Å2 / Biso mean: 50.48 Å2 / Biso min: 19.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2---1.77 Å20 Å2
3---3.55 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.33 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 0 62 3156
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.222.5
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 (%)
2.6-2.720.3581528.90.29115340.0231710168698.6
2.72-2.860.3531659.70.26115280.021708169399.1
2.86-3.040.2811508.80.25315470.0211709169799.3
3.04-3.280.3351709.80.24415480.0191726171899.5
3.28-3.60.3061639.40.22915710.0181737173499.8
3.6-4.120.2391649.40.1815810.0141746174599.9
4.12-5.190.21623012.80.1715470.0111796177798.9
5.19-28.540.2731779.10.22417210.0171936189898
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4acy.paramacy.top

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