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- PDB-1pp0: volvatoxin A2 in monoclinic crystal -

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Basic information

Entry
Database: PDB / ID: 1pp0
Titlevolvatoxin A2 in monoclinic crystal
Componentsvolvatoxin A2
KeywordsTOXIN / volvatoxin A2 / ingot crystal form
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
ACETIC ACID / Volvatoxin A2
Similarity search - Component
Biological speciesVolvariella volvacea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 ...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
B: volvatoxin A2
C: volvatoxin A2
D: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,20917
Polymers89,4284
Non-polymers78113
Water13,619756
1
A: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6576
Polymers22,3571
Non-polymers3005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5374
Polymers22,3571
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4172
Polymers22,3571
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: volvatoxin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5975
Polymers22,3571
Non-polymers2404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.983, 57.478, 114.629
Angle α, β, γ (deg.)90.00, 119.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
volvatoxin A2


Mass: 22356.961 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Volvariella volvacea (fungus) / References: UniProt: Q6USC4
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.27 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate, PEG 4000, acetate buffer, 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: 0.9236 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9236 Å / Relative weight: 1
ReflectionResolution: 1.4→29.85 Å / Num. all: 172073 / Num. obs: 146871 / % possible obs: 85.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 24.5 Å2 / Limit h max: 81 / Limit h min: -108 / Limit k max: 41 / Limit k min: -108 / Limit l max: 81 / Limit l min: 0 / Observed criterion F max: 895251.86 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.036 / Net I/σ(I): 26
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2 / % possible all: 49.1

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Processing

Software
NameVersionClassification
ADSCquantum softwaredata collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IW3

1iw3
PDB Unreleased entry


Resolution: 1.42→29.85 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6898 5.1 %RANDOM
Rwork0.229 ---
all-164652 --
obs-136219 82.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 68.7373 Å2 / ksol: 0.394891 e/Å3
Displacement parametersBiso max: 116.37 Å2 / Biso mean: 30.32 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å25.41 Å2
2---6.88 Å20 Å2
3---6.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Luzzati d res high-1.42
Refinement stepCycle: LAST / Resolution: 1.42→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6148 0 0 808 6956
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it2.271.5
X-RAY DIFFRACTIONc_mcangle_it3.262
X-RAY DIFFRACTIONc_scbond_it4.182
X-RAY DIFFRACTIONc_scangle_it5.832.5
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 (%)
1.42-1.480.36261730.342117630.014205011238060.4
1.48-1.560.3237453.60.296132730.011205311401868.3
1.56-1.660.297613.70.275143990.01205221516073.9
1.66-1.790.2838384.10.26156470.009205671648580.1
1.79-1.970.2549114.40.239170600.008205421797187.5
1.97-2.250.27110094.90.244188820.008205921989196.6
2.25-2.840.262104150.234193710.007206652041298.8
2.84-29.850.2329764.70.205189260.007209581990295
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4acy.param

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