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- PDB-1hxj: CRYSTAL STRUCTURE OF THE MAIZE ZM-P60.1 BETA-GLUCOSIDASE -

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Basic information

Entry
Database: PDB / ID: 1hxj
TitleCRYSTAL STRUCTURE OF THE MAIZE ZM-P60.1 BETA-GLUCOSIDASE
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION
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
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: 2.05 Å
AuthorsVevodova, J. / Su, X.-D. / Marek, J. / Brzobohaty, B.
Citation
Journal: Plant Physiol. / Year: 2001
Title: Insights into the functional architecture of the catalytic center of a maize beta-glucosidase Zm-p60.1
Authors: Zouhar, J. / Vevodova, J. / Marek, J. / Damborsky, J. / Su, X.-D. / Brzobohaty, B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Purification, Crystallization and Preliminary X-Ray Analysis of a Maize Cytokinin-Glucoside-Specific Beta-Glucosidase
Authors: Vevodova, J. / Marek, J. / Zouhar, J. / Brzobohaty, B. / Su, X.-D.
History
DepositionJan 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,0022
Polymers116,0022
Non-polymers00
Water16,376909
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.664, 110.718, 72.940
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe second part of the biological assembly is generated by the two fold axis parallel to the a-axis

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Components

#1: Protein BETA-GLUCOSIDASE / E.C.3.2.1.21 / GENTIOBIASE / CELLOBIASE / BETA-D-GLUCOSIDE GLUCOHYDROLASE


Mass: 58000.918 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: PRSET A / Gene (production host): ZM-P60.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS CELLS / References: UniProt: P49235, beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O
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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4000, 0.1 M citrate buffer pH 5.6, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 294K
Crystal grow
*PLUS
Method: unknown / PH range low: 5.9 / PH range high: 5.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-25 %(w/v)PEG400011
20.1 Mcitrate11pH5.3-5.9
3ammonium acetate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9831 / Wavelength: 0.9831 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2000
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9831 Å / Relative weight: 1
ReflectionResolution: 2.05→68 Å / Num. all: 52651 / Num. obs: 52651 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.048 / Net I/σ(I): 15.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 4.9 / Num. unique all: 4711 / Rsym value: 0.174 / % possible all: 85.7
Reflection
*PLUS
Lowest resolution: 68 Å / % possible obs: 94.7 % / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Lowest resolution: 2.18 Å / % possible obs: 85.7 % / Rmerge(I) obs: 0.176

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CBG

1cbg


Resolution: 2.05→34.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 983707.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3036 6.1 %RANDOM
Rwork0.168 ---
all-55455 --
obs-52651 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.35 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.83 Å20 Å27.99 Å2
2---5.54 Å20 Å2
3---0.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Luzzati d res high-2.05
Refinement stepCycle: LAST / Resolution: 2.05→34.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7958 0 0 909 8867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 427 5.7 %
Rwork0.2 7067 -
obs--81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Refinement
*PLUS
Lowest resolution: 68 Å / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rwork: 0.2

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