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- PDB-6fpd: AB21 protein from Agaricus bisporus -

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Basic information

Entry
Database: PDB / ID: 6fpd
TitleAB21 protein from Agaricus bisporus
ComponentsProtein AB21
KeywordsUNKNOWN FUNCTION / Agaricus bisporus / tetrahelical bundle / toxin-like
Function / homologyProtein AB21
Function and homology information
Biological speciesAgaricus bisporus (cultivated mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHouser, J. / Demo, G. / Komarek, J. / Wimmerova, M.
CitationJournal: Proteins / Year: 2018
Title: Structure and properties of AB21, a novel Agaricus bisporus protein with structural relation to bacterial pore-forming toxins.
Authors: Komarek, J. / Ivanov Kavkova, E. / Houser, J. / Horackova, A. / Zdanska, J. / Demo, G. / Wimmerova, M.
History
DepositionFeb 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein AB21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6573
Polymers22,5721
Non-polymers852
Water73941
1
A: Protein AB21
hetero molecules

A: Protein AB21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3146
Polymers45,1442
Non-polymers1704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area2790 Å2
ΔGint-48 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.936, 73.936, 70.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Protein AB21


Mass: 22572.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agaricus bisporus (cultivated mushroom)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E160*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 20 mM MES, 150 mM NaCl, pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→36.96 Å / Num. obs: 7689 / % possible obs: 99.9 % / Redundancy: 11.5 % / Biso Wilson estimate: 20.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 40.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 12 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 26.7 / Num. unique obs: 1113 / CC1/2: 0.998 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→36.96 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.822 / SU B: 15.369 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 0.634 / ESU R Free: 0.363 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31719 383 5 %RANDOM
Rwork0.24346 ---
obs0.24723 7274 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.887 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å2-0.79 Å2-0 Å2
2---1.57 Å20 Å2
3---5.1 Å2
Refinement stepCycle: 1 / Resolution: 2.5→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 5 41 1468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191448
X-RAY DIFFRACTIONr_bond_other_d0.0020.021366
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9431974
X-RAY DIFFRACTIONr_angle_other_deg0.91933127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92224.42661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16215220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.25159
X-RAY DIFFRACTIONr_chiral_restr0.0580.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2973.029762
X-RAY DIFFRACTIONr_mcbond_other1.2933.029761
X-RAY DIFFRACTIONr_mcangle_it2.2624.535949
X-RAY DIFFRACTIONr_mcangle_other2.2614.536950
X-RAY DIFFRACTIONr_scbond_it1.0533.104686
X-RAY DIFFRACTIONr_scbond_other1.0523.104686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8744.6291026
X-RAY DIFFRACTIONr_long_range_B_refined4.223.861671
X-RAY DIFFRACTIONr_long_range_B_other4.19923.8711672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 31 -
Rwork0.328 540 -
obs--100 %

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