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- PDB-1e4n: Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) b... -

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Basic information

Entry
Database: PDB / ID: 1e4n
TitleCrystal structure of the inactive mutant Monocot (Maize ZMGlu1) beta-glucosidase ZMGluE191D in complex with the natural aglycone DIMBOA
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION / INACTIVE MUTANT E191D / HYDROLASE COMPLEX WITH DIMBOA
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
Chem-HBO / 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: 2.1 Å
AuthorsCzjzek, M. / Cicek, M. / Bevan, D.R. / Zamboni, V. / Henrissat, B. / Esen, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / 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 11, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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)117,3394
Polymers116,9172
Non-polymers4222
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.570, 95.310, 117.760
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: (-0.82128, 0.36548, -0.43809), (0.38059, -0.22107, -0.89793), (-0.42502, -0.90419, 0.04246)
Vector: 56.63911, 60.4344, 75.64961)

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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): PLYS S / References: UniProt: P49235, beta-glucosidase
#2: Chemical ChemComp-HBO / 2,4-DIHYDROXY-7-(METHYLOXY)-2H-1,4-BENZOXAZIN-3(4H)-ONE


Mass: 211.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION GLU191ASP
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: 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: 2.1→29.1 Å / Num. obs: 58526 / % possible obs: 96.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.083 / Rsym value: 0.068 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.386 / % possible all: 90.3
Reflection shell
*PLUS
% possible obs: 90.3 %

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Processing

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

1e1e


Resolution: 2.1→29 Å / Data cutoff high absF: 1000000 / Cross valid method: THROUGHOUT / σ(F): 0.1
Details: THE N- AND C-TERMINAL RESIDUES WERE NOT SEEN IN THE ELECTRON DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2962 5 %RANDOM
Rwork0.223 ---
obs0.223 58462 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.15 Å2 / ksol: 0.3556 e/Å3
Displacement parametersBiso mean: 38.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-6 Å
Luzzati sigma a0.51 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.1→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7916 0 30 436 8382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0073
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_deg1.36
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.822
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: 0.306 Å / Weight position: 5
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.506 275 4.6 %
Rwork0.504 4873 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DIMBOA.PARAMDIMBOA.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.266 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.822

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