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- PDB-4re3: Different transition state conformations for the hydrolysis of be... -

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Basic information

Entry
Database: PDB / ID: 4re3
TitleDifferent transition state conformations for the hydrolysis of beta-mannosides and beta-glucosides in the rice Os7BGlu26 family GH1 beta-mannosidase/beta-glucosidase
ComponentsBeta-mannosidase/beta-glucosidase
KeywordsHYDROLASE / GH1
Function / homology
Function and homology information


beta-D-fucosidase activity / beta-mannosidase activity / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GLUCOIMIDAZOLE / beta-glucosidase / beta-glucosidase
Similarity search - Component
Biological speciesOryza sativa Indica Group (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTankrathok, A. / Iglesias-Fernandez, J. / Williams, R.J. / Hakki, Z. / Robinson, R.C. / Hrmova, M. / Rovira, C. / Williams, S.J. / Ketudat Cairns, J.R.
CitationJournal: ACS CATALYSIS / Year: 2015
Title: A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides
Authors: Tankrathok, A. / Iglesias-Fernandez, J. / Williams, R.J. / Pengthaisong, S. / Baiya, S. / Hakki, Z. / Robinson, R.C. / Hrmova, M. / Rovira, C. / Williams, S.J. / Ketudat Cairns, J.R.
History
DepositionSep 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-mannosidase/beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6348
Polymers57,7041
Non-polymers9307
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.100, 73.209, 134.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-mannosidase/beta-glucosidase / Os7BGlu26


Mass: 57703.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice)
Plasmid: pET32A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettagami DE3
References: UniProt: B5ABY0, UniProt: A2YPH1*PLUS, beta-mannosidase

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Non-polymers , 5 types, 126 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GIM / GLUCOIMIDAZOLE / (5S,6S,7R,8R)-5-(HYDROXYMETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL


Mass: 201.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 0.8M K/Na tartrate, 0.1 M HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 22658 / Num. obs: 22658 / % possible obs: 99.9 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.55→2.64 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JHO

4jho


Resolution: 2.55→24.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.318 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21316 1153 5.1 %RANDOM
Rwork0.17527 ---
obs0.17725 21454 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2--1.87 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.55→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 61 119 4114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224184
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.945689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98523.052213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64815631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4381528
X-RAY DIFFRACTIONr_chiral_restr0.0970.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023312
X-RAY DIFFRACTIONr_nbd_refined0.2040.21957
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.28
X-RAY DIFFRACTIONr_mcbond_it0.8851.52497
X-RAY DIFFRACTIONr_mcangle_it1.09523927
X-RAY DIFFRACTIONr_scbond_it1.89231994
X-RAY DIFFRACTIONr_scangle_it2.7044.51762
LS refinement shellResolution: 2.545→2.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 83 -
Rwork0.211 1547 -
obs--98.97 %

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