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- PDB-1ex1: BETA-D-GLUCAN EXOHYDROLASE FROM BARLEY -

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Basic information

Entry
Database: PDB / ID: 1ex1
TitleBETA-D-GLUCAN EXOHYDROLASE FROM BARLEY
ComponentsPROTEIN (BETA-D-GLUCAN EXOHYDROLASE ISOENZYME EXO1)
KeywordsHYDROLASE / CELL WALL DEGRADATION
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase / beta-glucosidase activity / extracellular region
Similarity search - Function
Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / : / beta-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.2 Å
AuthorsVarghese, J.N. / Hrmova, M. / Fincher, G.B.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Three-dimensional structure of a barley beta-D-glucan exohydrolase, a family 3 glycosyl hydrolase.
Authors: Varghese, J.N. / Hrmova, M. / Fincher, G.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-Ray Analysis of Beta-D-Glucan Exohydrolase Isoenzyme Exo1 from Barley (Hordeum Vulgare); a Family 3 Glycosyl Hydrolase
Authors: Varghese, J.N. / Hrmova, M. / Hoj, P.B. / Fincher, G.B.
History
DepositionNov 10, 1998Processing site: RCSB
Revision 1.0Nov 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: PROTEIN (BETA-D-GLUCAN EXOHYDROLASE ISOENZYME EXO1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9754
Polymers65,4761
Non-polymers1,4993
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.090, 102.090, 184.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (BETA-D-GLUCAN EXOHYDROLASE ISOENZYME EXO1) / E.C.3.2.1.58 / EXO1 / EXOGLUCANASE


Mass: 65475.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THREE GLYCSYLATED SITES AT ASN 221, 498, 600 GLUCOSE BOUND IN PUTATIVE ACTIVE SITE
Source: (natural) Hordeum vulgare (barley) / Organ: GERMINATING SEED
References: GenBank: AAD23382, UniProt: Q9XEI3*PLUS, glucan 1,3-beta-glucosidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1098.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6DManpa1-4DGlcpNAcb1-4[DFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2112m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-3-1/a3-b1_a4-c1_c4-d1_d6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: 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


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
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.83 Å3/Da / Density % sol: 66 %
Description: THE SAME CRYSTAL WAS USED TO COLLECT BOTH NATIVE AND PIP DATA
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277-279 K / Method: vapor diffusion, hanging drop / Details: Hrmova, M., (1998) Acta Cryst., D54, 687.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.8 mg/mlenzyme1drop
275 mMHEPES-NaOH1drop
37.5 mMsodium acetate1drop
41.2 %(w/v)PEG4001drop
50.8 Mammonium sulfate1drop
61.7 Mammonium sulfate1reservoir
750 mMHEPES-NaOH1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 408526 / % possible obs: 78 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.1
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 2.8 / % possible all: 37.8
Reflection
*PLUS
Num. obs: 40310 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Num. measured all: 148526
Reflection shell
*PLUS
% possible obs: 32 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PROTEINmodel building
SHARPphasing
REFMACrefinement
PROTEINphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→20 Å / SU B: 4.29 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2128 5 %RANDOM
Rwork0.17 ---
obs-39456 83.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 99 220 4885
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5712
X-RAY DIFFRACTIONp_mcangle_it2.3153
X-RAY DIFFRACTIONp_scbond_it2.2442
X-RAY DIFFRACTIONp_scangle_it3.2943
X-RAY DIFFRACTIONp_plane_restr0.01380.03
X-RAY DIFFRACTIONp_chiral_restr0.120.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2550.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1370.3
X-RAY DIFFRACTIONp_planar_tor87
X-RAY DIFFRACTIONp_staggered_tor17.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.320
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.283 / Rfactor Rwork: 0.202 / Num. reflection obs: 1633 / Rfactor obs: 0.202

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