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- PDB-8hj8: Crystal structure of barley exohydrolase isoform ExoI E220A mutan... -

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Basic information

Entry
Database: PDB / ID: 8hj8
TitleCrystal structure of barley exohydrolase isoform ExoI E220A mutant in complex with 2-deoxy-2-fluoro-D-glucopyranosides
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 / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-beta-D-glucopyranose / Beta-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)68,26225
Polymers65,8361
Non-polymers2,42624
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint3 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.500, 100.500, 182.689
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 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

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Sugars , 3 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
#3: Sugar ChemComp-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Sugar ChemComp-SHG / 2-deoxy-2-fluoro-beta-D-glucopyranose / 2-deoxy-2-fluoro-beta-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 648 molecules

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


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


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 3.5 Å3/Da / Density % sol: 64.89 %
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: 1.95→88.06 Å / Num. obs: 64687 / % possible obs: 100 % / Redundancy: 28.2 % / CC1/2: 0.997 / Net I/σ(I): 38.7
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 64687 / CC1/2: 0.997

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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: 1.95→88.06 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 5.083 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18406 3452 5.1 %RANDOM
Rwork0.14368 ---
obs0.14572 64687 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.339 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å2-0 Å2
3----2.97 Å2
Refinement stepCycle: 1 / Resolution: 1.95→88.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 154 629 5375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0194858
X-RAY DIFFRACTIONr_bond_other_d0.0020.024630
X-RAY DIFFRACTIONr_angle_refined_deg2.5121.9826572
X-RAY DIFFRACTIONr_angle_other_deg1.629310659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92323.878196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14715776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2291530
X-RAY DIFFRACTIONr_chiral_restr0.1620.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215423
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021055
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_it2.7043.1242434
X-RAY DIFFRACTIONr_mcbond_other2.5773.1042422
X-RAY DIFFRACTIONr_mcangle_it3.1444.6363027
X-RAY DIFFRACTIONr_mcangle_other3.1454.6373028
X-RAY DIFFRACTIONr_scbond_it4.3753.6152424
X-RAY DIFFRACTIONr_scbond_other4.1263.592413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5635.2363528
X-RAY DIFFRACTIONr_long_range_B_refined7.28127.596070
X-RAY DIFFRACTIONr_long_range_B_other6.97826.4495711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.953→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 260 -
Rwork0.21 4682 -
obs--98.72 %
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)
10.3705-0.1443-0.1930.07720.13680.5201-0.06750.0012-0.0540.03240.0290.02780.02820.08460.03850.01670.00790.01310.04030.01240.03924.35916.256429.703
20.1441-0.3156-0.13590.7410.28340.7591-0.01690.0558-0.05140.0223-0.07390.0816-0.0132-0.07080.09080.0078-0.0220.0070.0804-0.03760.05510.936920.489216.1778
30.3784-0.2246-0.27780.13990.18710.3977-0.0474-0.03040.020.02510.00980.00250.03370.03250.03770.02690.0040.0040.0326-0.00710.03922.529331.710651.3296
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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