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- PDB-7d6b: Crystal structure of Oryza sativa Os4BGlu18 monolignol beta-gluco... -

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Basic information

Entry
Database: PDB / ID: 7d6b
TitleCrystal structure of Oryza sativa Os4BGlu18 monolignol beta-glucosidase with delta-gluconolactone
ComponentsBeta-glucosidase 18
KeywordsHYDROLASE / monolignol beta-glucosidase / Os4BGlu18 / delta-gluconolactone
Function / homology
Function and homology information


coniferin metabolic process / coniferin beta-glucosidase activity / glycoside metabolic process / beta-D-fucosidase activity / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
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
D-glucono-1,5-lactone / Beta-glucosidase 18
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBaiya, S. / Pengthaisong, S. / Ketudat Cairns, J.R.
Funding support Thailand, 2items
OrganizationGrant numberCountry
Other governmentBRG5980015 Thailand Research fund and Suranaree University of Technology Thailand
Other governmentSuranaree University of Technology Thailand
CitationJournal: Plos One / Year: 2021
Title: Structural analysis of rice Os4BGlu18 monolignol beta-glucosidase.
Authors: Baiya, S. / Pengthaisong, S. / Kitjaruwankul, S. / Ketudat Cairns, J.R.
History
DepositionSep 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase 18
B: Beta-glucosidase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,55921
Polymers110,6642
Non-polymers1,89519
Water11,043613
1
A: Beta-glucosidase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,33911
Polymers55,3321
Non-polymers1,00710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,22010
Polymers55,3321
Non-polymers8889
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.109, 83.831, 207.448
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A24 - 500
2114B24 - 500

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Components

#1: Protein Beta-glucosidase 18 / Os4bglu18


Mass: 55331.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: BGLU18, Os04g0513900, LOC_Os04g43410, OSJNBa0004N05.26, OSJNBb0070J16.3
Production host: Escherichia coli (E. coli) / References: UniProt: Q7XSK0, beta-glucosidase
#2: Sugar ChemComp-LGC / D-glucono-1,5-lactone / (3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE / GLUCONOLACTONE


Type: D-saccharide / Mass: 178.140 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 19% PEG 3350, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 53787 / % possible obs: 98.9 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 26.3
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 5317 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RGL

2rgl


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.389 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 2676 5 %RANDOM
Rwork0.1451 ---
obs0.1467 50803 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.13 Å2 / Biso mean: 19.825 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2--1.02 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7715 0 121 613 8449
Biso mean--32.63 26.8 -
Num. residues----952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198095
X-RAY DIFFRACTIONr_bond_other_d0.0020.027298
X-RAY DIFFRACTIONr_angle_refined_deg1.351.95110978
X-RAY DIFFRACTIONr_angle_other_deg0.959316783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92623.101416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.746151229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4261560
X-RAY DIFFRACTIONr_chiral_restr0.0780.21121
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022030
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7345 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.360.5
MEDIUM THERMAL2.012
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 197 -
Rwork0.148 3689 -
all-3886 -
obs--99.49 %

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