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- PDB-1e55: Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) b... -

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Basic information

Entry
Database: PDB / ID: 1.0E+55
TitleCrystal structure of the inactive mutant Monocot (Maize ZMGlu1) beta-glucosidase ZMGluE191D in complex with the competitive inhibitor dhurrin
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION / INACTIVE MUTANT E191D / COMPLEX WITH DHURRIN
Function / homology
Function and homology information


galactosidase activity / fucosidase activity / xylanase activity / DIMBOA glucoside beta-D-glucosidase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / cytokinin-activated signaling pathway / mannosidase activity / cellulose 1,4-beta-cellobiosidase activity / beta-glucosidase / beta-glucosidase activity ...galactosidase activity / fucosidase activity / xylanase activity / DIMBOA glucoside beta-D-glucosidase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / cytokinin-activated signaling pathway / mannosidase activity / cellulose 1,4-beta-cellobiosidase activity / beta-glucosidase / beta-glucosidase activity / chloroplast / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / (2S)-HYDROXY(4-HYDROXYPHENYL)ETHANENITRILE / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic
Similarity search - Component
Biological speciesZEA MAYS (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCzjzek, M. / Cicek, M. / Bevan, D.R. / Zamboni, V. / Henrissat, B. / Esen, A.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2000
Title: The mechanism of substrate (aglycone) specificity in beta-glucosidases is revealed by crystal structures of mutant maize beta-glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes.
Authors: Czjzek, M. / Cicek, M. / Zamboni, V. / Bevan, D.R. / Henrissat, B. / Esen, A.
#1: Journal: Biotechnol.Bioeng. / Year: 1999
Title: Expression of Soluble and Catalytically Active Plant (Monocot) Beta-Glucosidases in E. Coli
Authors: Cicek, M. / Esen, A.
History
DepositionJul 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-GLUCOSIDASE
B: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5756
Polymers116,9172
Non-polymers6594
Water10,845602
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint4.9 kcal/mol
Surface area33670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.800, 95.000, 117.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8236, 0.36629, -0.43302), (0.37298, -0.22538, -0.90005), (-0.42727, -0.90279, 0.04901)
Vector: 57.07482, 60.46521, 75.30616)

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Components

#1: Protein BETA-GLUCOSIDASE


Mass: 58458.422 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZEA MAYS (maize) / Strain: CV. MUTIN / Tissue: COLEOPTILE / Organelle: CHLOROPLAST / Plasmid: PET-21A / Gene (production host): GLU1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): PLYSS / References: UniProt: P49235, beta-glucosidase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-DHR / (2S)-HYDROXY(4-HYDROXYPHENYL)ETHANENITRILE


Mass: 149.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION GLU191ASP
Has protein modificationY
Sequence detailsTHE N- AND C-TERMINAL RESID. WERE NOT SEEN IN DENSITY MAPS

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growpH: 7.5 / Details: 22 % PEG 4000, 5 % ISOPROPANOL, 0.1 M HEPES PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES1reservoir
222 %PEG40001reservoir
35 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorDate: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→29.1 Å / Num. obs: 69098 / % possible obs: 98.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.117 / Rsym value: 0.084 / Net I/σ(I): 6.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.284 / % possible all: 97.1
Reflection shell
*PLUS
% possible obs: 97.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E1E

1e1e


Resolution: 2→29 Å / Data cutoff high absF: 1000000 / Cross valid method: THROUGHOUT / σ(F): 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3513 5 %RANDOM
Rwork0.196 ---
obs0.196 69029 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.17 Å2 / ksol: 0.3604 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-6 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7948 0 44 602 8594
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.902
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSRms dev position: 0.274 Å / Weight position: 5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.327 342 4.9 %
Rwork0.309 6284 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE-DHUR.PARAMCARBOHYDRATE-DHUR.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.902

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