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- PDB-1pp6: VVA2 (STRIP CRYSTAL FORM) -

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Basic information

Entry
Database: PDB / ID: 1pp6
TitleVVA2 (STRIP CRYSTAL FORM)
ComponentsVolvatoxin A2
KeywordsTOXIN / Volvatoxin A2 / strip crystal form
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / 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
Biological speciesVolvariella volvacea (paddy straw mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
DepositionJun 16, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Volvatoxin A2
D: Volvatoxin A2
E: Volvatoxin A2


Theoretical massNumber of molelcules
Total (without water)111,7855
Polymers111,7855
Non-polymers00
Water21612
1
A: Volvatoxin A2


Theoretical massNumber of molelcules
Total (without water)22,3571
Polymers22,3571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Volvatoxin A2


Theoretical massNumber of molelcules
Total (without water)22,3571
Polymers22,3571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Volvatoxin A2


Theoretical massNumber of molelcules
Total (without water)22,3571
Polymers22,3571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Volvatoxin A2


Theoretical massNumber of molelcules
Total (without water)22,3571
Polymers22,3571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Volvatoxin A2


Theoretical massNumber of molelcules
Total (without water)22,3571
Polymers22,3571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.672, 80.679, 107.853
Angle α, β, γ (deg.)90.00, 105.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Volvatoxin A2


Mass: 22356.961 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Volvariella volvacea (paddy straw mushroom)
References: UniProt: Q6USC4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.79 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium cacodylate, PEG 8000, glycerol, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1.0446
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0446 Å / Relative weight: 1
ReflectionResolution: 3.18→28.54 Å / Num. all: 20087 / Num. obs: 19692 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.3
Reflection shellResolution: 3.2→3.24 Å / Rmerge(I) obs: 0.472 / % possible all: 99.9

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Processing

Software
NameClassification
ADSCdata collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PP0

1pp0


Resolution: 3.2→28.54 Å / Rfactor Rfree error: 0.008 / 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
Rfree0.348 1817 9.8 %RANDOM
Rwork0.264 ---
all-19764 --
obs-18485 93.5 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 35.69 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 82.68 Å2
Baniso -1Baniso -2Baniso -3
1-20.06 Å20 Å222.99 Å2
2---9.95 Å20 Å2
3----10.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.88 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.2→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 0 12 7686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
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 (%)
3.2-3.350.4822369.60.37820280.0232454226492.3
3.35-3.520.4472068.40.30821070.0212462231393.9
3.52-3.740.4322068.40.32319350.0222459214187.1
3.74-4.030.3312229.10.22520770.0152451229993.8
4.03-4.430.2952108.60.22918270.0162444203783.3
4.43-5.070.269249100.222050.0132480245499
5.07-6.380.3972419.70.29822180.0182485245998.9
6.38-28.540.3382479.70.27322710.0182534251899.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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