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- PDB-6jgp: Crystal structure of barley exohydrolaseI W434H mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 6jgp
TitleCrystal structure of barley exohydrolaseI W434H mutant in complex with methyl 6-thio-beta-gentiobioside.
ComponentsBETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO
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 6-THIO-BETA-GENTIOBIOSIDE / ACETATE ION / Uncharacterized protein / beta-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare subsp. vulgare (domesticated barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 14, 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

Downloads & links

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Assembly

Deposited unit
A: BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,60116
Polymers65,8461
Non-polymers1,75515
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint0 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.132, 100.132, 181.202
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 GLUCOHYDROLASE ISOENZYME EXO


Mass: 65846.000 Da / Num. of mol.: 1 / Mutation: W434H
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-(1-6)-methyl 6-thio-beta-D-glucopyranoside / METHYL 6-THIO-BETA-GENTIOBIOSIDE


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 6-THIO-BETA-GENTIOBIOSIDE
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5]/1-2/a6-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp6SH]{[(6+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 , 5 types, 503 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / 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 / Comment: precipitant*YM
#7: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsLys320 is confirmed by DNA sequencing result. However, the electron density map is not clear, ...Lys320 is confirmed by DNA sequencing result. 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: 3.45 Å3/Da / Density % sol: 64.34 %
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: 1.99→87.64 Å / Num. obs: 60320 / % possible obs: 99.7 % / Redundancy: 28 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 26.8
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 0.856 / Num. unique obs: 118063

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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: 1.99→48.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.879 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19093 3220 5.1 %RANDOM
Rwork0.15382 ---
obs0.15568 60320 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.768 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-0 Å20 Å2
2--0.88 Å20 Å2
3----1.76 Å2
Refinement stepCycle: 1 / Resolution: 1.99→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 101 490 5183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194766
X-RAY DIFFRACTIONr_bond_other_d0.0010.024553
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.986465
X-RAY DIFFRACTIONr_angle_other_deg0.9753.00110468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20324.063192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04515765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7691528
X-RAY DIFFRACTIONr_chiral_restr0.1210.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021034
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.992→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 230 -
Rwork0.188 4224 -
obs--96.12 %
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)
10.4043-0.1003-0.20320.03130.06280.395-0.0669-0.0176-0.070.01980.00740.02330.00760.07790.05950.01990.00750.01730.04680.02210.023624.54216.325329.6773
20.9094-0.7472-0.96370.95920.43311.41230.03970.1086-0.0421-0.0424-0.05810.0488-0.0462-0.11510.01840.0184-0.02210.00120.0783-0.02110.010111.137320.657416.0473
30.3101-0.1831-0.2660.1260.12780.3884-0.0272-0.04010.01090.00720.004-0.00310.01960.04850.02320.03090.00680.00080.0465-0.00830.01942.659431.418551.2618
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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