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- PDB-6jge: Crystal structure of barley exohydrolaseI W434A mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 6jge
TitleCrystal structure of barley exohydrolaseI W434A mutant in complex with methyl 2-thio-beta-sophoroside.
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 2-THIO-BETA-SOPHOROSIDE / Uncharacterized protein / beta-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare subsp. vulgare (domesticated barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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: Data collection / Database references ...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 / 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)68,76127
Polymers65,7791
Non-polymers2,98226
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-145 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.826, 100.826, 180.990
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: 65778.938 Da / Num. of mol.: 1 / Mutation: W434A
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, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-2)-methyl 2-thio-beta-D-glucopyranoside / METHYL 2-THIO-BETA-SOPHOROSIDE


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 2-THIO-BETA-SOPHOROSIDE
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5]/1-2/a2-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp2SH]{[(2+S)][b-D-Glcp]{}}}LINUCSPDB-CARE
#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.: 1
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 , 4 types, 600 molecules

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


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsAmino acid at the position 320 should be Lysine. However, the electron density map is not clear, ...Amino acid at the position 320 should be Lysine. However, the electron density map is not clear, probably side chain of this residue is flexible

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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: 3.5 Å3/Da / Density % sol: 64.82 %
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: 1.92→88.08 Å / Num. obs: 67919 / % possible obs: 99.9 % / Redundancy: 29 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 28.5
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.141 / Num. unique obs: 4913

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Processing

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

3wli


Resolution: 1.92→46.1 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.564 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 3624 5.1 %RANDOM
Rwork0.14 ---
obs0.141 67919 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 96.1 Å2 / Biso mean: 20.707 Å2 / Biso min: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å20 Å2
2--0.58 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 1.92→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 177 576 5340
Biso mean--47.77 31.1 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194865
X-RAY DIFFRACTIONr_bond_other_d0.0010.024664
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9916581
X-RAY DIFFRACTIONr_angle_other_deg1.2723.00110733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24523.897195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40415778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7681530
X-RAY DIFFRACTIONr_chiral_restr0.0820.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021048
LS refinement shellResolution: 1.923→1.973 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 267 -
Rwork0.181 4913 -
all-5180 -
obs--99.29 %
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)
10.4398-0.0947-0.21240.06320.09020.4337-0.07810.0078-0.06250.03070.02240.02020.00820.060.05570.02880.01380.01630.06660.02140.073524.841816.622129.5925
22.077-1.5991-1.05611.33610.99451.78850.01460.2701-0.14670.0052-0.11340.0904-0.0308-0.14050.09870.00790.0106-0.01050.1428-0.03060.047611.523520.802516.0432
30.4285-0.2568-0.28380.16490.15660.3705-0.0299-0.02890.01370.0122-0.00160.00830.00690.03420.03140.03510.0163-0.00040.0712-0.00240.06952.716531.855251.1214
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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