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- PDB-6md6: CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 6md6
TitleCRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH METHYL 2-THIO-BETA-SOPHOROSIDE
ComponentsBeta-D-glucan exohydrolase isoenzyme ExoI
KeywordsHYDROLASE / BETA BARREL / GRAIN DEVELOPMENT / TIM BARREL/BETA SHEET / N-GLYCOSYLATION / PLANT APOPLAST
Function / homology
Function and homology information


glucan catabolic process / beta-glucosidase / beta-glucosidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / membrane => GO:0016020 / carbohydrate metabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / 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 / TIM Barrel ...Glycoside hydrolase family 3 C-terminal domain / Glycoside hydrolase, family 3, N-terminal domain / 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 / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHYL 2-THIO-BETA-SOPHOROSIDE / Uncharacterized protein / beta-glucosidase
Similarity search - Component
Biological speciesHordeum vulgare subsp. vulgare (domesticated barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsStreltsov, V.A. / Luang, S. / Hrmova, M.
CitationJournal: Nat Commun / Year: 2019
Title: Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site.
Authors: Streltsov, V.A. / Luang, S. / Peisley, A. / Varghese, J.N. / Ketudat Cairns, J.R. / Fort, S. / Hijnen, M. / Tvaroska, I. / Arda, A. / Jimenez-Barbero, J. / Alfonso-Prieto, M. / Rovira, C. / ...Authors: Streltsov, V.A. / Luang, S. / Peisley, A. / Varghese, J.N. / Ketudat Cairns, J.R. / Fort, S. / Hijnen, M. / Tvaroska, I. / Arda, A. / Jimenez-Barbero, J. / Alfonso-Prieto, M. / Rovira, C. / Mendoza, F. / Tiessler-Sala, L. / Sanchez-Aparicio, J.E. / Rodriguez-Guerra, J. / Lluch, J.M. / Marechal, J.D. / Masgrau, L. / Hrmova, M.
History
DepositionSep 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)69,47323
Polymers65,8941
Non-polymers3,57922
Water18,0691003
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.311, 100.311, 182.153
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: 65894.070 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 26-630 / Mutation: N345K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare subsp. vulgare (domesticated barley)
Plasmid: PPICZALPHABNH8/DEST / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD11680H / References: UniProt: A0A287SCR5, UniProt: Q9XEI3*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-2)-methyl 2-thio-beta-D-glucopyranoside / METHYL 2-THIO-BETA-SOPHOROSIDE


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 2-THIO-BETA-SOPHOROSIDE
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5]/1-2/a2-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp2SH]{[(2+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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 4 types, 1021 molecules

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


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1003 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS STATE THERE IS AN ERROR IN THE CDNA SEQUENCING OF AF102868 (GENBANK ACCESSION NUMBER). ...THE AUTHORS STATE THERE IS AN ERROR IN THE CDNA SEQUENCING OF AF102868 (GENBANK ACCESSION NUMBER). RESIDUE 320 (SEQUENCE DATABASE RESIDUE 345) IS LYS AND IS NOT ASN.

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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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 75MM HEPES-NAOH PH7.0, 1.2% PEG 400, 1.7M AMMONIUM SULPHATE , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
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: 1.68→48.36 Å / Num. obs: 101119 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 29.2 % / Rmerge(I) obs: 0.076 / Rsym value: 0.074 / Net I/σ(I): 39.19
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 28 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 4 / Rsym value: 0.75 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IEQ

1ieq


Resolution: 1.68→46.13 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.412 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15902 5311 5 %RANDOM
Rwork0.1321 ---
obs0.13347 101119 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.527 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.68→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 172 1003 5751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0134858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174537
X-RAY DIFFRACTIONr_angle_refined_deg2.2821.6686570
X-RAY DIFFRACTIONr_angle_other_deg1.9071.60110523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9155603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54921.982227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97415774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1691531
X-RAY DIFFRACTIONr_chiral_restr0.1260.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02975
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_it1.281.22415
X-RAY DIFFRACTIONr_mcbond_other1.281.1992414
X-RAY DIFFRACTIONr_mcangle_it1.8911.7963017
X-RAY DIFFRACTIONr_mcangle_other1.8911.7973018
X-RAY DIFFRACTIONr_scbond_it2.8431.6382443
X-RAY DIFFRACTIONr_scbond_other2.8431.6382444
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0132.3093554
X-RAY DIFFRACTIONr_long_range_B_refined7.42519.6726024
X-RAY DIFFRACTIONr_long_range_B_other6.85817.0875644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.678→1.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 374 -
Rwork0.201 7313 -
obs--99 %
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)
10.3854-0.1513-0.23110.07660.15450.5685-0.07910.0072-0.05350.03440.03340.03640.01960.09780.04570.0340.01220.01380.09850.01380.071324.329716.376529.8306
20.7737-0.7976-0.30091.51230.46780.58-0.01140.3338-0.09870.115-0.15060.01630.0087-0.17770.16190.01620.0245-0.01740.2168-0.09540.069110.999820.464616.1219
30.4317-0.2675-0.30310.16920.20450.4197-0.0587-0.03690.01630.0290.01610.00160.01560.03180.04260.06090.01090.00480.0887-0.01010.07032.492831.775151.1592
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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