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- PDB-1v08: Crystal structure of the Zea maze beta-glucosidase-1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 1v08
TitleCrystal structure of the Zea maze beta-glucosidase-1 in complex with gluco-tetrazole
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / BETA-GLUCOSIDASE / GLYCOSIDE HYDROLASE / DIMBOA-GLUCOSIDE / INHIBITOR / PEST DEFENSE / FAMILY GH1 / CHLOROPLAST / TRANSIT PEPTIDE
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 / : / beta-glucosidase ...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 / : / 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
NOJIRIMYCINE TETRAZOLE / 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: 1.9 Å
AuthorsMoriniere, J. / Verdoucq, L. / Bevan, D.R. / Esen, A. / Henrissat, B. / Czjzek, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Determinants of Substrate Specificity in Family 1 Beta-Glucosidases: Novel Insights from the Crystal Structure of Sorghum Dhurrinase-1, a Plant Beta-Glucosidase with Strict ...Title: Structural Determinants of Substrate Specificity in Family 1 Beta-Glucosidases: Novel Insights from the Crystal Structure of Sorghum Dhurrinase-1, a Plant Beta-Glucosidase with Strict Specificity, in Complex with its Natural Substrate
Authors: Verdoucq, L. / Moriniere, J. / Bevan, D.R. / Esen, A. / Vasella, A. / Henrissat, B. / Czjzek, M.
History
DepositionMar 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)117,7266
Polymers116,9172
Non-polymers8094
Water15,115839
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.180, 104.800, 119.340
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: (-0.20717, -0.35231, -0.91267), (-0.36927, -0.83573, 0.40643), (-0.90594, 0.42122, 0.04304)
Vector: 4.19313, 98.01054, -35.20337)

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Components

#1: Protein BETA-GLUCOSIDASE / CHLOROPLAST PRECURSOR / GENTIOBIASE / CELLOBIASE / BETA-D-GLUCOSIDE GLUCOHYDROLASE


Mass: 58458.422 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ZEA MAYS (maize) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49235, beta-glucosidase
#2: Chemical
ChemComp-NTZ / NOJIRIMYCINE TETRAZOLE


Mass: 202.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A AND B, GLU 245 TO ASP CATALYTIC ACTIVITY: HYDROLYSIS OF TERMINAL, ...ENGINEERED MUTATION IN CHAIN A AND B, GLU 245 TO ASP CATALYTIC ACTIVITY: HYDROLYSIS OF TERMINAL, NON-REDUCING BETA-D- GLUCOSE RESIDUES WITH RELEASE OF BETA-D-GLUCOSE.
Sequence detailsASP A 191, SITE DIRECTED MUTATION

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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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growpH: 7.5 / Details: 22% PEG 4000, 5% ISOPROPANOL, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorDate: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→29.8 Å / Num. obs: 92037 / % possible obs: 96.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.9
Reflection shellResolution: 1.95→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.5 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E1E

1e1e


Resolution: 1.9→29.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.826 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4604 5 %RANDOM
Rwork0.173 ---
obs0.175 87352 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2--2.88 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7934 0 56 839 8829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218238
X-RAY DIFFRACTIONr_bond_other_d0.0020.027012
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.94811192
X-RAY DIFFRACTIONr_angle_other_deg0.895316402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21134
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029224
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021762
X-RAY DIFFRACTIONr_nbd_refined0.20.21843
X-RAY DIFFRACTIONr_nbd_other0.2370.28306
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.24182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2683
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4751.54880
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90827860
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41333358
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3414.53332
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 294
Rwork0.279 5950

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