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- PDB-5dzg: Crystal Structure of the catalytic nucleophile mutant of VvEG16 i... -

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Basic information

Entry
Database: PDB / ID: 5dzg
TitleCrystal Structure of the catalytic nucleophile mutant of VvEG16 in complex with a xyloglucan tetradecasaccharide
ComponentsVvEG16, endo-glucanase
KeywordsHYDROLASE / cell wall / dietary fiber / mixed-linkage glucan / xyloglucan / beta-glucan / glycoside hydrolase / endo-glucanase / grapes / plants / protein structure / GH16 / beta-jelly roll / phylogeny
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Beta-glucanase/XTH / Beta-glucanase / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
GH16 domain-containing protein
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsMcGregor, N.G.S. / Tung, C.C. / Van Petegem, F. / Brumer, H.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Plant J. / Year: 2017
Title: Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases.
Authors: McGregor, N. / Yin, V. / Tung, C.C. / Van Petegem, F. / Brumer, H.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.3Dec 11, 2019Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.type
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VvEG16, endo-glucanase
B: VvEG16, endo-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9594
Polymers46,7882
Non-polymers3,1712
Water6,702372
1
A: VvEG16, endo-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5022
Polymers23,3941
Non-polymers2,1081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VvEG16, endo-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4572
Polymers23,3941
Non-polymers1,0631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.277, 78.957, 132.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VvEG16, endo-glucanase


Mass: 23394.051 Da / Num. of mol.: 2 / Fragment: endo-glucanase / Mutation: E88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: VIT_15s0048g01850 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Hi-control / References: UniProt: F6I323
#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 2107.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,14,13/[a2122h-1a_1-5][a2122h-1b_1-5][a212h-1a_1-5]/1-2-2-2-2-2-2-2-3-3-3-3-3-3/a4-b1_b4-c1_b6-n1_c4-d1_c6-m1_d4-e1_d6-l1_e4-f1_f4-g1_f6-k1_g4-h1_g6-j1_h6-i1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1a_1-5][a2122h-1b_1-5][a212h-1a_1-5]/1-2-2-2-3-3-3/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.1 %
Description: clear, colourless, tetragonal bipyramidal crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10 mg/mL Glc8 XyGOs, 1 mM EDTA, 100 mM pH 6 MES, 20% PEG 6000
PH range: 5.5-6.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2014 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.79→39.41 Å / Num. obs: 40942 / % possible obs: 98.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.317 / % possible all: 78.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
Blu-Ice0.1.26data collection
XDSJanuary 10, 2014data scaling
XSCALEJanuary 10, 2014data scaling
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UMZ

1umz


Resolution: 1.79→39.41 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 2055 5.03 %
Rwork0.171 --
obs0.173 38822 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.7 Å2
Refinement stepCycle: LAST / Resolution: 1.79→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 215 372 3662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123444
X-RAY DIFFRACTIONf_angle_d1.4794731
X-RAY DIFFRACTIONf_dihedral_angle_d15.081188
X-RAY DIFFRACTIONf_chiral_restr0.269556
X-RAY DIFFRACTIONf_plane_restr0.007574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7902-1.83190.28521160.2252000X-RAY DIFFRACTION78
1.8319-1.87770.24811280.19832519X-RAY DIFFRACTION95
1.8777-1.92850.2359980.17282628X-RAY DIFFRACTION100
1.9285-1.98520.23461280.16792584X-RAY DIFFRACTION99
1.9852-2.04930.2171320.16852596X-RAY DIFFRACTION100
2.0493-2.12250.21331730.17352561X-RAY DIFFRACTION100
2.1225-2.20750.23451170.16512637X-RAY DIFFRACTION100
2.2075-2.3080.21670.1652598X-RAY DIFFRACTION100
2.308-2.42960.22351290.1662636X-RAY DIFFRACTION100
2.4296-2.58180.23931360.17782635X-RAY DIFFRACTION100
2.5818-2.78110.22471450.18562623X-RAY DIFFRACTION99
2.7811-3.06090.23021430.18622612X-RAY DIFFRACTION99
3.0609-3.50360.23191390.172675X-RAY DIFFRACTION100
3.5036-4.41320.17281580.15592679X-RAY DIFFRACTION100
4.4132-39.42190.21941460.16212840X-RAY DIFFRACTION99

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