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- PDB-4iis: Crystal structure of a glycosylated beta-1,3-glucanase (HEV B 2),... -

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Basic information

Entry
Database: PDB / ID: 4iis
TitleCrystal structure of a glycosylated beta-1,3-glucanase (HEV B 2), An allergen from Hevea Brasiliensis (Space group P41)
ComponentsBeta-1,3-glucanase form 'RRII Gln 2'
KeywordsHYDROLASE / Allergen / glycoprotein / glycoside hydrolase / GH17 family / pathogenesis-related class-2 protein / TIM-barrel / glycosidase / carbohydrate/sugar binding / piroglutamate (n-terminal residue) / latex
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
CACODYLATE ION / CITRATE ANION / glucan endo-1,3-beta-D-glucosidase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6676 Å
AuthorsRodriguez-Romero, A. / Hernandez-Santoyo, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural analysis of the endogenous glycoallergen Hev b 2 (endo-beta-1,3-glucanase) from Hevea brasiliensis and its recognition by human basophils.
Authors: Rodriguez-Romero, A. / Hernandez-Santoyo, A. / Fuentes-Silva, D. / Palomares, L.A. / Munoz-Cruz, S. / Yepez-Mulia, L. / Orozco-Martinez, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and identification of the glycosylated moieties of two isoforms of the main allergen Hev b 2 and preliminary X-ray analysis of two polymorphs of isoform II.
Authors: Fuentes-Silva, D. / Mendoza-Hernandez, G. / Stojanoff, V. / Palomares, L.A. / Zenteno, E. / Torres-Larios, A. / Rodriguez-Romero, A.
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionNov 27, 2013ID: 3F55
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-glucanase form 'RRII Gln 2'
B: Beta-1,3-glucanase form 'RRII Gln 2'
C: Beta-1,3-glucanase form 'RRII Gln 2'
D: Beta-1,3-glucanase form 'RRII Gln 2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,42810
Polymers141,2764
Non-polymers1,1526
Water1,00956
1
A: Beta-1,3-glucanase form 'RRII Gln 2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8344
Polymers35,3191
Non-polymers5153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,3-glucanase form 'RRII Gln 2'


Theoretical massNumber of molelcules
Total (without water)35,3191
Polymers35,3191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-1,3-glucanase form 'RRII Gln 2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7663
Polymers35,3191
Non-polymers4472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-1,3-glucanase form 'RRII Gln 2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5082
Polymers35,3191
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.118, 150.118, 77.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein
Beta-1,3-glucanase form 'RRII Gln 2'


Mass: 35319.047 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hevea brasiliensis (rubber tree) / Strain: GV-42
References: UniProt: D1M8S7, glucan endo-1,3-beta-D-glucosidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 61 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M trisodium citrate dihydrate, 0.1M sodium cacodylate, 30% (w/v) 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 27, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.61→47.473 Å / Num. all: 52459 / Num. obs: 49364 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 58.37 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.61-2.763.60.6291.9193.9
2.76-2.923.60.4162.9195.7
2.92-3.123.60.2644.3193.8
3.12-3.383.60.1617194.8
3.38-3.73.60.09410.6194.4
3.7-4.133.60.0615.7194

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1238)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HPG

4hpg


Resolution: 2.6676→47.471 Å / Isotropic thermal model: ISOTROPIC / σ(F): 1.34 / Phase error: 25.94 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2196 2352 5.08 %
Rwork0.2015 --
obs0.2022 46257 93.52 %
all-52372 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6676→47.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9887 0 73 56 10016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110217
X-RAY DIFFRACTIONf_angle_d1.63613922
X-RAY DIFFRACTIONf_dihedral_angle_d13.5463740
X-RAY DIFFRACTIONf_chiral_restr0.0741518
X-RAY DIFFRACTIONf_plane_restr0.0111814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6676-2.7220.41271610.34662599X-RAY DIFFRACTION90
2.722-2.78110.36121390.31832563X-RAY DIFFRACTION90
2.7811-2.84580.29041300.29842617X-RAY DIFFRACTION91
2.8458-2.91690.34811380.29382588X-RAY DIFFRACTION90
2.9169-2.99580.25441450.27482582X-RAY DIFFRACTION89
2.9958-3.08390.27871240.26352608X-RAY DIFFRACTION90
3.0839-3.18330.29751460.24812609X-RAY DIFFRACTION90
3.1833-3.2970.23621260.23082538X-RAY DIFFRACTION89
3.297-3.42890.25811380.2142601X-RAY DIFFRACTION89
3.4289-3.58480.24321410.21042583X-RAY DIFFRACTION89
3.5848-3.77350.21181390.18092561X-RAY DIFFRACTION89
3.7735-4.00960.191500.17822554X-RAY DIFFRACTION88
4.0096-4.31860.1841420.15722558X-RAY DIFFRACTION88
4.3186-4.75220.17721150.15232573X-RAY DIFFRACTION89
4.7522-5.43730.16411610.15892529X-RAY DIFFRACTION87
5.4373-6.84110.18231330.19282563X-RAY DIFFRACTION87
6.8411-33.76610.14851070.15282614X-RAY DIFFRACTION87

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