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

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Basic information

Entry
Database: PDB / ID: 4hpg
TitleCrystal structure of a glycosylated beta-1,3-glucanase (HEV B 2), an allergen from Hevea brasiliensis
ComponentsBeta-1,3-glucanase
KeywordsHYDROLASE / ALLERGEN / glycoprotein / glycoside hydrolase / gh17 family / pathogenesis-related class-2 protein / tim barrel / glycosidase hydrolase / carbohydrate/sugar binding / glycosylation / pyroglutamic acid (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 / Glycosyl hydrolases family 17 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / (1->3)-beta-glucan endohydrolase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5364 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
DepositionOct 23, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionNov 27, 2013ID: 3EM5
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-glucanase
B: Beta-1,3-glucanase
C: Beta-1,3-glucanase
D: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4449
Polymers141,2764
Non-polymers1,1685
Water3,477193
1
B: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6862
Polymers35,3191
Non-polymers3671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0144
Polymers35,3191
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,3191
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-1,3-glucanase


Theoretical massNumber of molelcules
Total (without water)35,3191
Polymers35,3191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.176, 89.778, 101.542
Angle α, β, γ (deg.)90.00, 113.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-1,3-glucanase


Mass: 35319.047 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Para Rubber Tree latex / Source: (natural) Hevea brasiliensis (rubber tree) / Strain: GV-42
References: UniProt: A2TM14, glucan endo-1,3-beta-D-glucosidase
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 0.1M trisodium citrate dihydrate, 30%(W/V) polyethylene glycol 4000., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 15, 2007 / Details: MIRRORS
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→25.5 Å / Num. all: 49816 / Num. obs: 48122 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.642.80.1345.1180.7
3.54-3.954.30.0659.71100
3.95-4.564.30.05710.41100
4.56-5.594.30.056101100
5.59-7.914.30.0616.41100
7.91-25.2140.1034.2196.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CYG

2cyg


Resolution: 2.5364→25.208 Å / SU ML: 0.3 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 1878 4.05 %
Rwork0.1928 --
obs0.1948 46317 97.14 %
all-49816 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5364→25.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9938 0 76 193 10207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110281
X-RAY DIFFRACTIONf_angle_d1.48513998
X-RAY DIFFRACTIONf_dihedral_angle_d13.9563751
X-RAY DIFFRACTIONf_chiral_restr0.071530
X-RAY DIFFRACTIONf_plane_restr0.011812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5364-2.60490.29761100.24152679X-RAY DIFFRACTION76
2.6049-2.68140.3191110.23743149X-RAY DIFFRACTION90
2.6814-2.76790.29441530.23933421X-RAY DIFFRACTION98
2.7679-2.86670.33091470.2363487X-RAY DIFFRACTION100
2.8667-2.98130.30921530.24033544X-RAY DIFFRACTION100
2.9813-3.11670.29141570.23533471X-RAY DIFFRACTION100
3.1167-3.28070.29241290.23913534X-RAY DIFFRACTION100
3.2807-3.48580.2451480.21773507X-RAY DIFFRACTION100
3.4858-3.75410.23161630.1923502X-RAY DIFFRACTION100
3.7541-4.13040.20861520.16583514X-RAY DIFFRACTION100
4.1304-4.72470.19711600.14813517X-RAY DIFFRACTION100
4.7247-5.93980.19511340.16093567X-RAY DIFFRACTION100
5.9398-25.20910.20441610.16213547X-RAY DIFFRACTION99

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