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- PDB-1e1f: Crystal structure of a Monocot (Maize ZMGlu1) beta-glucosidase in... -

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Basic information

Entry
Database: PDB / ID: 1e1f
TitleCrystal structure of a Monocot (Maize ZMGlu1) beta-glucosidase in complex with p-Nitrophenyl-beta-D-thioglucoside
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION / PNP-BETA-D-THIOGLUCOSIDE
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-nitrophenyl 1-thio-beta-D-glucopyranoside / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCzjzek, M. / Cicek, M. / Bevan, D.R. / Henrissat, B. / Esen, A.
CitationJournal: 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.
History
DepositionMay 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 1.5Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 1.6Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5804
Polymers116,9452
Non-polymers6352
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-7.62 kcal/mol
Surface area34840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.640, 118.150, 80.880
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97447, -0.16779, -0.14917), (0.16313, 0.07268, 0.98392), (-0.15425, -0.98314, 0.09819)
Vector: 41.14678, -56.62112, 35.72366)

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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 / Cell (production host): PLYS S CELLS / Gene (production host): GLU1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49235, beta-glucosidase
#2: Sugar ChemComp-PSG / 4-nitrophenyl 1-thio-beta-D-glucopyranoside / PARA-NITROPHENYL 1-THIO-BETA-D-GLUCOPYRANOSIDE / 4-nitrophenyl 1-thio-beta-D-glucoside / 4-nitrophenyl 1-thio-D-glucoside / 4-nitrophenyl 1-thio-glucoside


Type: D-saccharide / Mass: 317.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO7S
IdentifierTypeProgram
para-nitrophenyl-1-thio-b-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INHIBITOR IN THE ACTIVE SITE IS DISORDERED AND PROBABLY PRESENT IN MORE THAN THE TWO DEPOSITED ...THE INHIBITOR IN THE ACTIVE SITE IS DISORDERED AND PROBABLY PRESENT IN MORE THAN THE TWO DEPOSITED CONFORMATIONS. THE TWO CONFORMATIONS CORRESPOND TO THOSE OF LOW ENERGY AND THE DISTORTED SKEW-BOAT CONFORMATION NECESSARY FOR THE CATALYTIC MECANISM
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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growpH: 5.6
Details: 27 % PEG 4000, 1.5 % 1,2,3-HEPTANETRIOL 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE PH 5.6
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
61.5 %1,2,3-heptanetriol1drop
75 mMpNPTGlc1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorDate: Mar 15, 1999
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 340923 / % possible obs: 99 % / Redundancy: 3.1 % / Rsym value: 0.094 / Net I/σ(I): 4.2
Reflection shellResolution: 2.59→2.65 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.263 / % possible all: 97.5
Reflection
*PLUS
Num. obs: 34732 / % possible obs: 99.8 % / Num. measured all: 137688 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 1.8

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Processing

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

1cbg


Resolution: 2.6→39 Å / Data cutoff high absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1332 3.9 %RANDOM
Rwork0.199 ---
obs0.199 34384 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.93 Å2 / ksol: 0.2966 e/Å3
Displacement parametersBiso mean: 22.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-6 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.6→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7934 0 42 356 8332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
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_deg1.33
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.62
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.862
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: 0.395 Å / Weight position: 10
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.275 3093 -
obs--90.57 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2INHA-BOAT.PARINHA-2.TOP
X-RAY DIFFRACTION3INHA-CHAIR.PAR
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_deg22.62
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.862

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