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- PDB-8hj7: Crystal structure of barley exohydrolase isoform ExoI E220A mutan... -

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Basic information

Entry
Database: PDB / ID: 8hj7
TitleCrystal structure of barley exohydrolase isoform ExoI E220A mutant in complex with beta-D-glucopyranose.
ComponentsBeta-D-glucan exohydrolase isoenzyme ExoI
KeywordsHYDROLASE / Barley exohydrolaseI / enzyme function
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
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 / beta-D-glucopyranose / Beta-D-glucan exohydrolase isoenzyme ExoI
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLuang, S. / Streltsov, V.A. / Hrmova, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other government Australia
CitationJournal: Commun Biol / Year: 2025
Title: The structure and dynamics of water molecule networks underlie catalytic efficiency in a glycoside exo-hydrolase.
Authors: Luang, S. / Fernandez-Luengo, X. / Streltsov, V.A. / Marechal, J.D. / Masgrau, L. / Hrmova, M.
History
DepositionNov 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-D-glucan exohydrolase isoenzyme ExoI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,38620
Polymers65,1381
Non-polymers2,24819
Water12,592699
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.634, 100.634, 182.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 exohydrolase isoenzyme ExoI


Mass: 65138.211 Da / Num. of mol.: 1 / Mutation: E220A
Source method: isolated from a genetically manipulated source
Details: This protein sequence contains the expression tag (His-3 to Ala-0), and engineered mutation residue is E220A. Whole protein sequence was confirmed by DNA sequencing.
Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9XEI3

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Sugars , 2 types, 5 molecules

#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 713 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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: Mar 3, 2010 / 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: 1.85→88.1 Å / Num. obs: 74941 / % possible obs: 98 % / Redundancy: 26 % / CC1/2: 0.998 / Net I/σ(I): 50.8
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 74941 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
REFMAC7.0.005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WLI

3wli


Resolution: 1.85→88.1 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.262 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18397 3965 5 %RANDOM
Rwork0.14331 ---
obs0.14534 74941 97.57 %-
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 mean: 45.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å2-0 Å2-0 Å2
2--2.27 Å2-0 Å2
3----4.53 Å2
Refinement stepCycle: 1 / Resolution: 1.85→88.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 133 699 5404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0194797
X-RAY DIFFRACTIONr_bond_other_d0.0020.024563
X-RAY DIFFRACTIONr_angle_refined_deg2.4861.9826506
X-RAY DIFFRACTIONr_angle_other_deg1.196310500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06524.031191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89115761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.541528
X-RAY DIFFRACTIONr_chiral_restr0.1550.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215367
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021037
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8183.6752422
X-RAY DIFFRACTIONr_mcbond_other2.7823.662414
X-RAY DIFFRACTIONr_mcangle_it3.2775.4693017
X-RAY DIFFRACTIONr_mcangle_other3.2775.473018
X-RAY DIFFRACTIONr_scbond_it4.574.1552375
X-RAY DIFFRACTIONr_scbond_other4.4114.122356
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9236.0393460
X-RAY DIFFRACTIONr_long_range_B_refined7.61432.6826044
X-RAY DIFFRACTIONr_long_range_B_other7.42231.1045637
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.895 Å
RfactorNum. reflection% reflection
Rfree0.296 232 -
Rwork0.249 4499 -
obs--80.31 %
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)
10.3663-0.1585-0.19510.08640.14440.5953-0.08220.0035-0.05110.04090.03050.04280.03480.11150.05170.02310.00720.01610.05590.01710.092424.56616.529429.9308
20.7252-0.9396-0.82791.34190.80741.57980.0140.1243-0.0805-0.0074-0.14050.0625-0.0279-0.130.12650.0118-0.0218-0.0060.0792-0.03380.092511.104520.573816.1984
30.3784-0.2174-0.27630.12880.17680.4813-0.0515-0.0260.02760.02810.01160.00230.04580.03180.03980.03180.00110.00950.034-0.00640.10012.578731.765251.3212
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 357
2X-RAY DIFFRACTION2A358 - 373
3X-RAY DIFFRACTION3A374 - 602

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