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- PDB-6jg2: Crystal structure of barley exohydrolaseI wildtype in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6jg2
TitleCrystal structure of barley exohydrolaseI wildtype in complex with 4'-nitrophenyl thiolaminaribioside
ComponentsBarley exohydrolase I
KeywordsHYDROLASE / Barley exohydrolaseI / enzyme function
Function / homology
Function and homology information


beta-glucosidase / membrane => GO:0016020 / hydrolase activity, hydrolyzing O-glycosyl compounds / 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
Chem-BV6 / Uncharacterized protein / beta-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare subsp. vulgare (domesticated barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Mar 23, 2022Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_detector ...database_2 / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.details / _diffrn_detector.detector / _diffrn_detector.type / _diffrn_radiation.monochromator / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type / _software.name
Revision 1.2Oct 5, 2022Group: 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
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Barley exohydrolase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,24513
Polymers65,8941
Non-polymers2,35112
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-5 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.178, 100.178, 182.514
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 / Sugars , 2 types, 3 molecules A

#1: Protein Barley exohydrolase I


Mass: 65894.070 Da / Num. of mol.: 1
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
#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.: 2
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, 350 molecules

#3: Chemical ChemComp-BV6 / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-(4-nitrophenoxy)-3,5-bis(oxidanyl)oxan-4-yl]sulfanyl-oxane-3,4,5-triol


Mass: 479.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25NO12S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
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: 3.47 Å3/Da / Density % sol: 64.6 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 16, 2013 / Details: Osmic VariMax
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→87.82 Å / Num. obs: 58669 / % possible obs: 97.23 % / Redundancy: 24 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 27.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.835 / Num. unique obs: 4122

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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: 2→41.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.341 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 3140 5.1 %RANDOM
Rwork0.1808 ---
obs0.1831 58669 97.23 %-
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: 114.01 Å2 / Biso mean: 42.362 Å2 / Biso min: 26.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å2-0 Å2
2--1.88 Å20 Å2
3----3.77 Å2
Refinement stepCycle: final / Resolution: 2→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4575 0 130 340 5045
Biso mean--70.63 47.38 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194801
X-RAY DIFFRACTIONr_bond_other_d0.0010.024583
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.9876508
X-RAY DIFFRACTIONr_angle_other_deg1.093.00110542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15924.063192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39415762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9571528
X-RAY DIFFRACTIONr_chiral_restr0.110.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.437 229 -
Rwork0.416 4122 -
obs--94.22 %
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)
10.3295-0.1251-0.20280.05070.07740.3447-0.0477-0.0364-0.04010.01860.01860.02780.01450.06180.02910.00890.00260.01460.0170.01720.121724.021316.375829.861
21.0176-1.0986-1.05531.27910.84832.0101-0.00140.0771-0.0311-0.0111-0.06210.01780.0571-0.13880.06360.0115-0.01520.00140.0293-0.02410.109810.610220.482416.2248
30.2438-0.1402-0.1890.08640.09530.4185-0.0181-0.02920.02320.00980.00930.00670.01260.05020.00880.00260.00470.00550.0168-0.00760.12262.23931.78651.2039
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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