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- PDB-1aq0: BARLEY 1,3-1,4-BETA-GLUCANASE IN MONOCLINIC SPACE GROUP -

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Basic information

Entry
Database: PDB / ID: 1aq0
TitleBARLEY 1,3-1,4-BETA-GLUCANASE IN MONOCLINIC SPACE GROUP
Components1,3-1,4-BETA-GLUCANASE
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOPROTEIN / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


licheninase activity / licheninase / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 17, plant / 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
ACETATE ION / Lichenase-2
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMueller, J.J. / Thomsen, K.K. / Heinemann, U.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of barley 1,3-1,4-beta-glucanase at 2.0-A resolution and comparison with Bacillus 1,3-1,4-beta-glucanase.
Authors: Muller, J.J. / Thomsen, K.K. / Heinemann, U.
#1: Journal: Plant Physiol.Biochem. (Paris) / Year: 1995
Title: Analysis of Glycan Structures of Barley (1-3,1-4)-Beta-D Glucan 4-Glucanohydrolase Isoenzyme Eii
Authors: Harthill, J.E. / Thomsen, K.K.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of Barley (1-3,1-4)-Beta-Glucanase, Isoenzyme II
Authors: Keitel, T. / Thomsen, K.K. / Heinemann, U.
History
DepositionAug 5, 1997Processing site: BNL
Revision 1.0Feb 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / software / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _software.name / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
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: 1,3-1,4-BETA-GLUCANASE
B: 1,3-1,4-BETA-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2506
Polymers64,2832
Non-polymers9674
Water7,530418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.580, 82.990, 77.560
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3572, 0.21075, -0.90994), (0.78786, 0.45529, 0.41472), (0.50169, -0.86504, -0.00342)
Vector: 12.98934, 2.88789, 73.42563)

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Components

#1: Protein 1,3-1,4-BETA-GLUCANASE / 1 / 3-1 / 4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE


Mass: 32141.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ISOENZYME 2 / Source: (natural) Hordeum vulgare (barley) / References: UniProt: P12257, licheninase
#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.: 2
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
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.41 Å3/Da / Density % sol: 25.2 %
Crystal growMethod: vapor diffusion / pH: 5.8
Details: PROTEIN SOLUTION: 20MM NAOAC/HOAC (PH 4.6), 2MM CACL2, C=60MG/ML. DROPLETS SIZE: 0.001 ML PROTEIN SOLUTION, 0.001 ML RESERVOIR SOLUTION; RESERVOIR SOLUTION: 100MM NAOAC/HOAC (PH 5.8), ...Details: PROTEIN SOLUTION: 20MM NAOAC/HOAC (PH 4.6), 2MM CACL2, C=60MG/ML. DROPLETS SIZE: 0.001 ML PROTEIN SOLUTION, 0.001 ML RESERVOIR SOLUTION; RESERVOIR SOLUTION: 100MM NAOAC/HOAC (PH 5.8), 20%(W/W) POLYETHYLENE GLYCOL 8000; VAPOUR DIFFUSION, FOUR DAYS, vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion / Details: Keitel, T., (1993) J.Mol.Biol., 232, 1003.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
260 mM1dropNaOAc
31 mM1dropCaCl2
410 %(w/w)PEG80001drop
5100 mM1reservoirNaOAc
620 %(w/w)PEG80001reservoir

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Data collection

DiffractionMean temperature: 294.2 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1992 / Details: PINHOLE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→13.65 Å / Num. obs: 40727 / % possible obs: 99.21 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 14.35 Å2 / Rsym value: 0.081
Reflection shellResolution: 2→2.09 Å / % possible all: 96.61
Reflection
*PLUS
Rmerge(I) obs: 0.081

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GHR

1ghr


Resolution: 2→13.6 Å / Rfactor Rfree error: 0.0058 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1363 3 %RANDOM
Rwork0.17 ---
obs0.17 40727 99.3 %-
Displacement parametersBiso mean: 14.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-13.6 Å
Refinement stepCycle: LAST / Resolution: 2→13.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4528 0 64 418 5010
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.314
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.184
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.1932 171 3 %
Rwork0.2089 4760 -
obs--96.61 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.184

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