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Basic information

Entry
Database: PDB / ID: 2cyg
TitleCrystal structure at 1.45- resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome
Componentsbeta-1, 3-glucananse
KeywordsHYDROLASE / endo-beta-1 / 3-glucanase / (beta-alpha)8-TIM-barrel / B-cell epitopes / allergen / banana
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolases family 17 signature. / Glycoside hydrolase family 17, plant / Glycoside hydrolase family 17 / Glycosyl hydrolases family 17 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glucan endo-1,3-beta-glucosidase
Similarity search - Component
Biological speciesMusa acuminata (dwarf banana)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsReceveur-Brechot, V. / Czjzek, M. / Barre, A. / Roussel, A. / Peumans, W.J. / Van Damme, E.J.M. / Rouge, P.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure at 1.45-A resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome
Authors: Receveur-Brechot, V. / Czjzek, M. / Barre, A. / Roussel, A. / Peumans, W.J. / Van Damme, E.J.M. / Rouge, P.
History
DepositionJul 7, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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: beta-1, 3-glucananse


Theoretical massNumber of molelcules
Total (without water)33,4421
Polymers33,4421
Non-polymers00
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.270, 53.930, 113.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein beta-1, 3-glucananse / endo-beta-1 / 3-glucanase


Mass: 33442.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Musa acuminata (dwarf banana)
References: UniProt: O22317, glucan endo-1,3-beta-D-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.034 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2002
RadiationMonochromator: single wavelength / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 53238 / Num. obs: 52014 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 10.46 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 13.4
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4819 / Rsym value: 0.129 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GHS

1ghs


Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.894 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 2644 5.1 %RANDOM
Rwork0.15722 ---
all0.15835 52014 --
obs0.15835 49317 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.92 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 0 407 2802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222455
X-RAY DIFFRACTIONr_bond_other_d0.0020.022174
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9423356
X-RAY DIFFRACTIONr_angle_other_deg0.78735063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015311
X-RAY DIFFRACTIONr_chiral_restr0.0670.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.1950.2457
X-RAY DIFFRACTIONr_nbd_other0.2290.22464
X-RAY DIFFRACTIONr_nbtor_other0.0780.21336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.242
X-RAY DIFFRACTIONr_mcbond_it0.3841.51563
X-RAY DIFFRACTIONr_mcangle_it0.76122523
X-RAY DIFFRACTIONr_scbond_it1.2063892
X-RAY DIFFRACTIONr_scangle_it1.9384.5833
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 194 -
Rwork0.16 3416 -
obs-3416 0.05 %

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