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- PDB-8hj6: Crystal structure of barley exohydrolase isoform ExoI E220A mutant -

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Basic information

Entry
Database: PDB / ID: 8hj6
TitleCrystal structure of barley exohydrolase isoform ExoI E220A mutant
ComponentsGlyco_hydro_3 domain-containing protein
KeywordsHYDROLASE / Barley exohydrolaseI / enzyme function
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / membrane
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-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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: Glyco_hydro_3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,44428
Polymers65,8361
Non-polymers2,60827
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-2 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.233, 100.233, 183.174
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 / Sugars , 2 types, 4 molecules A

#1: Protein Glyco_hydro_3 domain-containing protein


Mass: 65836.031 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: A0A8I6XKI1
#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

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Non-polymers , 5 types, 719 molecules

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


Mass: 238.278 Da / Num. of mol.: 2 / 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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 3.49 Å3/Da / Density % sol: 64.8 %
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: 1.79→87.93 Å / Num. obs: 79237 / % possible obs: 95.3 % / Redundancy: 24.8 % / CC1/2: 0.998 / Net I/σ(I): 48.6
Reflection shellResolution: 1.79→1.84 Å / Num. unique obs: 79237 / 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: 1.79→87.93 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.816 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18048 4186 5 %RANDOM
Rwork0.1416 ---
obs0.14355 79237 95.3 %-
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: 40.555 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å2-0 Å2-0 Å2
2--1.53 Å2-0 Å2
3----3.05 Å2
Refinement stepCycle: 1 / Resolution: 1.79→87.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 159 695 5446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0194856
X-RAY DIFFRACTIONr_bond_other_d0.0020.024654
X-RAY DIFFRACTIONr_angle_refined_deg2.4291.9796553
X-RAY DIFFRACTIONr_angle_other_deg1.762310703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.575605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22923.878196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75115776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.161530
X-RAY DIFFRACTIONr_chiral_restr0.1570.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215445
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021059
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_it2.6283.2222440
X-RAY DIFFRACTIONr_mcbond_other2.5053.192422
X-RAY DIFFRACTIONr_mcangle_it2.9654.7683027
X-RAY DIFFRACTIONr_mcangle_other2.9664.7693028
X-RAY DIFFRACTIONr_scbond_it4.4463.7032416
X-RAY DIFFRACTIONr_scbond_other4.433.7022413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5435.3953521
X-RAY DIFFRACTIONr_long_range_B_refined7.22928.7686093
X-RAY DIFFRACTIONr_long_range_B_other7.00827.2515677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 218 -
Rwork0.228 4127 -
obs--68.16 %
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)
10.3476-0.1189-0.26020.08490.15180.4959-0.071-0.0207-0.04390.02270.03470.02180.03640.07930.03640.01770.00990.01010.04970.01130.075324.348216.155929.7168
20.3995-0.4687-0.39470.57670.58551.39970.02090.1163-0.0503-0.0162-0.10780.0369-0.0326-0.11970.08680.0034-0.0065-0.00560.0857-0.02920.085810.938220.526116.2119
30.3066-0.1647-0.29240.09460.1750.3889-0.0367-0.02850.01720.0180.01060.01020.02570.04340.0260.02150.00680.00360.0485-0.00380.07432.579431.598951.4466
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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