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

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Basic information

Entry
Database: PDB / ID: 5dzf
TitleCrystal Structure of the catalytic nucleophile mutant of VvEG16 in complex with a mixed-linkage glucan octasaccharide
Componentsendo-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


licheninase / 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
beta-D-glucopyranose / Beta-glucanase
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMcGregor, N.G.S. / Tung, C.C. / Van Petegem, F. / Brumer, H.
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 1.1Nov 1, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_struct_oper_list / software
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 / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_special_symmetry / 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.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: endo-glucanase
B: endo-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0448
Polymers46,5942
Non-polymers2,4506
Water8,053447
1
A: endo-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1564
Polymers23,2971
Non-polymers8593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: endo-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8884
Polymers23,2971
Non-polymers1,5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.330, 74.330, 149.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-542-

HOH

31B-520-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein endo-glucanase


Mass: 23296.938 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

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Sugars , 3 types, 3 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1315.142 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,8,7/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_d4-e1_e4-f1_f3-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 450 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5 mM DTT, 5 mM G3GGG3GGG, 0.5 mM GG3GGG3GGG, 1 mM EDTA, 0.1 M HEPES, 1.6 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.8266 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 11, 2014
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium silicate flat mirror with Pt, Uncoated, and Pd strips
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.55→42.974 Å / Num. obs: 60997 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 23.527 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.205 / Rrim(I) all: 0.214 / Χ2: 0.995 / Net I/σ(I): 10.85 / Num. measured all: 738087
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.590.1043.250.4120052447041593.66793
1.59-1.630.1362.8080.5424169434042033.09996.8
1.63-1.680.1342.3830.7229250424542182.58299.4
1.68-1.730.2922.1060.9635160414541452.244100
1.73-1.790.5261.5731.5442601399039891.652100
1.79-1.850.7441.3252.2755072388438841.375100
1.85-1.920.8610.923.3655356373737370.952100
1.92-20.9260.6434.853805362636260.666100
2-2.090.9530.5066.1551304346534640.524100
2.09-2.190.9710.4027.849611335233520.416100
2.19-2.310.9790.3319.4746638315331530.343100
2.31-2.450.9860.27911.2944641302230220.289100
2.45-2.620.9910.22613.8641643282728270.234100
2.62-2.830.9930.17917.0638906265126510.186100
2.83-3.10.9970.12423.4936137247624760.129100
3.1-3.470.9990.08133.6232189221422140.084100
3.47-40.9990.05743.0828729199219920.059100
4-4.910.04351.3424309171517140.04599.9
4.9-6.930.9990.0544.9818775136213620.052100
6.9310.03852.3597408158090.03999.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSJanuary 10, 2014data scaling
XSCALEJanuary 10, 2014data scaling
PHASER2.5.5phasing
CootWinCoot-0.8.1.1model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UMZ

1umz


Resolution: 1.65→42.974 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 2558 5 %
Rwork0.1547 --
obs0.1571 51138 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.83 Å2 / Biso mean: 22.0494 Å2 / Biso min: 7.29 Å2
Refinement stepCycle: final / Resolution: 1.65→42.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 161 463 3761
Biso mean--21.37 35.36 -
Num. residues----405

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