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- PDB-1lq2: Crystal structure of barley beta-D-glucan glucohydrolase isoenzym... -

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Basic information

Entry
Database: PDB / ID: 1lq2
TitleCrystal structure of barley beta-D-glucan glucohydrolase isoenzyme Exo1 in complex with gluco-phenylimidazole
ComponentsBeta-D-glucan glucohydrolase isoenzyme Exo1
KeywordsHYDROLASE / 2-domain fold / ligand-protein complex
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
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 ...: / 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
Chem-IDD / : / Beta-D-glucan exohydrolase isoenzyme ExoI
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHrmova, M. / De Gori, R. / Smith, B.J. / Vasella, A. / Varghese, J.N. / Fincher, G.B.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Three-dimensional Structure of the Barley {beta}-D-Glucan Glucohydrolase in Complex with a Transition State Mimic.
Authors: Hrmova, M. / De Gori, R. / Smith, B.J. / Vasella, A. / Varghese, J.N. / Fincher, G.B.
History
DepositionMay 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / 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_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 / _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_atom_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 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 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The authors state there is an error in the cDNA sequencing of AF102868 (GenBank accession ...SEQUENCE The authors state there is an error in the cDNA sequencing of AF102868 (GenBank accession number). Residue 320 (sequence database residue 345) is a LYS and is not ASN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-D-glucan glucohydrolase isoenzyme Exo1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4746
Polymers65,0541
Non-polymers2,4205
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.693, 100.693, 182.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a monomer constructed from an (alpha/beta)8 barrel and an (alpha/beta)6 sandwich

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-D-glucan glucohydrolase isoenzyme Exo1 / beta-D-glucan exohydrolase isoenzyme ExoI


Mass: 65054.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Strain: Cultivar Clipper
References: GenBank: 4566505, UniProt: Q9XEI3*PLUS, glucan 1,3-beta-glucosidase

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Sugars , 3 types, 3 molecules

#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-L-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[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-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)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#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


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

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Non-polymers , 3 types, 243 molecules

#5: Chemical ChemComp-IDD / (5R,6R,7S,8S)-5-(HYDROXYMETHYL)-2-PHENYL-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL / GLUCO-PHENYLIMIDAZOLE


Mass: 276.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulphate, PEG 400, Sodium acetate, Hepes-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2001 / Details: Mono-capillary optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 24521 / % possible obs: 45.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.81 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.9
Reflection shellResolution: 2.62→2.69 Å / Rmerge(I) obs: 0.582 / % possible all: 61.1
Reflection
*PLUS
Num. obs: 44625 / % possible obs: 73.6 % / Num. measured all: 70377 / Rmerge(I) obs: 0.13
Reflection shell
*PLUS
% possible obs: 45.4 % / Rmerge(I) obs: 0.583

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1IEQ

1ieq


Resolution: 2.7→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 1015 Random
Rwork0.21 --
all-21173 -
obs-20158 -
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 163 241 4971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
Refinement
*PLUS
Highest resolution: 2.62 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2729 / Rfactor Rwork: 0.2096
Solvent computation
*PLUS
Displacement parameters
*PLUS

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