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

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Basic information

Entry
Database: PDB / ID: 6jgc
TitleCrystal structure of barley exohydrolaseI W286Y mutant in complex with glucose.
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
ACETATE ION / alpha-D-glucopyranose / Uncharacterized protein / beta-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare subsp. vulgare (domesticated barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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)70,29538
Polymers65,8711
Non-polymers4,42437
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-8 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.106, 100.106, 182.727
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 , 1 types, 1 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

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Sugars , 2 types, 4 molecules

#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 380 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 3.47 Å3/Da / Density % sol: 64.6 %
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: 2.36→48.32 Å / Num. obs: 36843 / % possible obs: 99.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 16.4
Reflection shellResolution: 2.363→2.424 Å / Rmerge(I) obs: 0.246 / Num. unique obs: 2651

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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: 2.36→48.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.068 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.175
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 1944 5 %RANDOM
Rwork0.1491 ---
obs0.1514 36843 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.69 Å2 / Biso mean: 27.143 Å2 / Biso min: 10.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2--0.28 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 2.36→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 249 347 5190
Biso mean--51.23 32.37 -
Num. residues----602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194890
X-RAY DIFFRACTIONr_bond_other_d0.0020.024641
X-RAY DIFFRACTIONr_angle_refined_deg2.032.0056614
X-RAY DIFFRACTIONr_angle_other_deg0.9033.00110663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7245601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47223.99193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61915766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.371529
X-RAY DIFFRACTIONr_chiral_restr0.1130.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021037
LS refinement shellResolution: 2.363→2.424 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 140 -
Rwork0.178 2651 -
all-2791 -
obs--99.15 %
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)
10.4057-0.0377-0.19990.06370.16940.4784-0.1219-0.047-0.0893-0.01010.02960.02770.00690.09530.09240.04530.01230.02270.05260.03110.030923.966916.623130.2365
21.4166-1.626-0.65892.03451.33572.4452-0.04080.1388-0.00860.0858-0.15080.03820.1073-0.14360.19160.0324-0.0189-0.00150.0668-0.04260.050210.608920.452416.3628
30.3994-0.2321-0.28430.14430.13420.4852-0.0472-0.04140.00240.01990.00980.0026-0.00420.05910.03740.04090.0058-0.0140.0506-0.01080.02352.106431.867851.3151
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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