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- PDB-1e1e: Crystal structure of a Monocot (Maize ZMGlu1) beta-glucosidase -

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Basic information

Entry
Database: PDB / ID: 1e1e
TitleCrystal structure of a Monocot (Maize ZMGlu1) beta-glucosidase
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION
Function / homology
Function and homology information


fucosidase activity / xylanase activity / galactosidase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / DIMBOA glucoside beta-D-glucosidase activity / cytokinin-activated signaling pathway / mannosidase activity / cellulose 1,4-beta-cellobiosidase activity / scopolin beta-glucosidase activity / beta-glucosidase activity ...fucosidase activity / xylanase activity / galactosidase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / DIMBOA glucoside beta-D-glucosidase activity / cytokinin-activated signaling pathway / mannosidase activity / cellulose 1,4-beta-cellobiosidase activity / scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / 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
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: 2.5 Å
AuthorsCzjzek, M. / Cicek, M. / Bevan, D.R. / Henrissat, B. / Esen, A.
Citation
Journal: Biochem.J. / Year: 2001
Title: Crystal Structure of a Monocotyledon (Maize Zmglu1) Beta-Glucosidase and a Model of its Complex with P-Nitrophenyl Beta-D-Thioglucoside
Authors: Czjzek, M. / Cicek, M. / Zamboni, V. / Burmeister, W.P. / Bevan, D.R. / Henrissat, B. / Esen, A.
#1: Journal: Plant Physiol. / Year: 1996
Title: Nucleotide Sequence of a Cdna Corresponding to a Second Beta-Glucosidase Gene in Maize
Authors: Bandaranayake, H. / Esen, A.
History
DepositionMay 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 16, 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 6, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,9452
Polymers116,9452
Non-polymers00
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-11.7 kcal/mol
Surface area35530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.880, 118.340, 77.100
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.88564, 0.35057, 0.30456), (-0.32182, -0.00949, 0.94675), (0.33479, -0.93649, 0.10441)
Vector: 32.21348, 27.02837, 32.03502)

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Components

#1: Protein BETA-GLUCOSIDASE /


Mass: 58472.445 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growpH: 5.6 / Details: 0.2 M AMMONIUM SULFATE, pH 5.60
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlenzyme1drop
220 mMHEPES1drop
30.1 Msodium citrate1reservoir
40.2 Mammonium acetate1reservoir
527 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorDate: Jan 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.42→29.1 Å / Num. obs: 549492 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.074 / Rsym value: 0.11 / Net I/σ(I): 6.4
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.207 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 27 Å / Num. obs: 42762 / % possible obs: 99.9 % / Num. measured all: 153615 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.276

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Processing

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

1cbg


Resolution: 2.5→27 Å / Data cutoff high absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.322 1900 5 %RANDOM
Rwork0.256 ---
obs0.256 38334 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.69 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 50.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.44 Å
Luzzati d res low-6 Å
Luzzati sigma a0.83 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.5→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7971 0 0 331 8302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0088
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_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.899
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: 0.362 Å / Weight position: 10
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.48 201 5 %
Rwork0.44 3750 -
obs--96.75 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.24 / Rfactor Rfree: 0.283
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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