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- PDB-6jgd: Crystal structure of barley exohydrolaseI W286Y mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 6jgd
TitleCrystal structure of barley exohydrolaseI W286Y mutant in complex with methyl 6-thio-beta-gentiobioside
ComponentsBETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1
KeywordsHYDROLASE / Barley exohydrolaseI / enzyme function
Function / homology
Function and homology information


beta-glucosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / membrane => GO:0016020 / carbohydrate metabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
METHYL 6-THIO-BETA-GENTIOBIOSIDE / ACETATE ION / Uncharacterized protein / beta-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare subsp. vulgare (domesticated barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsLuang, S. / Streltsov, V.A. / Hrmova, M.
CitationJournal: Nat Commun / Year: 2022
Title: The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases.
Authors: Luang, S. / Fernandez-Luengo, X. / Nin-Hill, A. / Streltsov, V.A. / Schwerdt, J.G. / Alonso-Gil, S. / Ketudat Cairns, J.R. / Pradeau, S. / Fort, S. / Marechal, J.D. / Masgrau, L. / Rovira, C. / Hrmova, M.
History
DepositionFeb 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_detector / diffrn_radiation / diffrn_source / exptl_crystal_grow / pdbx_unobs_or_zero_occ_residues / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.details / _diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _exptl_crystal_grow.pH / _software.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,55026
Polymers65,8711
Non-polymers3,67925
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-43 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.231, 101.231, 180.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1


Mass: 65871.031 Da / Num. of mol.: 1 / Mutation: W286Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare subsp. vulgare (domesticated barley)
Production host: Komagataella pastoris (fungus) / References: UniProt: A0A287SCR5, UniProt: Q9XEI3*PLUS
#2: Polysaccharide beta-D-glucopyranose-(1-6)-methyl 6-thio-beta-D-glucopyranoside / METHYL 6-THIO-BETA-GENTIOBIOSIDE


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 372.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: METHYL 6-THIO-BETA-GENTIOBIOSIDE
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5]/1-2/a6-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp6SH]{[(6+S)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 418 molecules

#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7 M ammonium sulfate, 75 mM HEPES-NaOH buffer, pH 7, containing 7.5 mM sodium acetate and 1.2% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2012 / Details: COLLIMATING MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.13→88.27 Å / Num. obs: 50439 / % possible obs: 99.9 % / Redundancy: 29.2 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 23
Reflection shellResolution: 2.13→2.19 Å / Rmerge(I) obs: 0.204 / Num. unique obs: 3637

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WLI

3wli


Resolution: 2.13→48.78 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.883 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.113
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1636 2702 5.1 %RANDOM
Rwork0.14 ---
obs0.1412 50439 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.17 Å2 / Biso mean: 23.498 Å2 / Biso min: 11.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0 Å2
2--0.48 Å20 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 2.13→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 154 394 5142
Biso mean--43.05 32.03 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194812
X-RAY DIFFRACTIONr_bond_other_d0.0010.024622
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9866497
X-RAY DIFFRACTIONr_angle_other_deg0.9933.00110637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09224.124194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6881528
X-RAY DIFFRACTIONr_chiral_restr0.0820.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021034
LS refinement shellResolution: 2.13→2.185 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.188 188 -
Rwork0.16 3637 -
all-3825 -
obs--99.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5103-0.0936-0.27260.03760.10720.4004-0.07270.0066-0.05950.02520.0250.01970.01990.04970.04770.04690.01860.01560.09490.01280.093424.996817.054329.8991
22.9192-2.0994-1.49211.58050.89821.5372-0.00560.2638-0.1270.0129-0.1090.0689-0.005-0.16210.11470.003-0.0028-0.00710.1695-0.02740.084811.601520.93616.0999
30.4544-0.2631-0.30770.15450.17690.4325-0.0349-0.01580.02250.01760-0.0023-0.0010.02940.03480.060.00980.00320.0886-0.00430.09132.726232.140850.9985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 357
2X-RAY DIFFRACTION2A358 - 373
3X-RAY DIFFRACTION3A374 - 602

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