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- PDB-5gqd: Crystal structure of covalent glycosyl-enzyme intermediate of xyl... -

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Basic information

Entry
Database: PDB / ID: 5gqd
TitleCrystal structure of covalent glycosyl-enzyme intermediate of xylanase mutant (T82A, N127S, and E128H) from Streptomyces olivaceoviridis E-86
ComponentsBeta-xylanase
KeywordsHYDROLASE / xylanase / mutant / pNP-xylobioside / covalent glycosyl-enzyme intermediate
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Ricin-type beta-trefoil lectin domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Ricin-type beta-trefoil lectin domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces olivaceoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSuzuki, R. / Fujimoto, Z. / Kaneko, S. / Kuno, A.
Citation
Journal: J.Appl.Glyosci. / Year: 2019
Title: Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant
Authors: Suzuki, R. / Fujimoto, Z. / Kaneko, S. / Hasegawa, T. / Kuno, A.
#1: Journal: J. Biochem. / Year: 2009
Title: Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86
Authors: Suzuki, R. / Fujimoto, Z. / Ito, S. / Kawahara, S. / Kaneko, S. / Taira, K. / Hasegawa, T. / Kuno, A.
History
DepositionAug 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.title / _citation.year
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.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 2.1Nov 8, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,78812
Polymers93,4862
Non-polymers1,30110
Water18,0331001
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-25 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.186, 94.045, 140.078
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 Beta-xylanase


Mass: 46743.207 Da / Num. of mol.: 2 / Mutation: T82A, N127S, E128H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria)
Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SI98, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a212h-1a_1-5][a212h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C5O3>]{[(1+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1001 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 25% ammonium sulfate 2% Mcllvaine buffer

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 5, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 94763 / % possible obs: 98.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 6.1 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D1Z

2d1z


Resolution: 1.8→40.09 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2814853.41 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4747 5 %RANDOM
Rwork0.175 ---
obs0.175 94683 98.2 %-
Solvent computationBsol: 73.9289 Å2 / ksol: 0.400613 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.09 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 790 5.1 %
Rwork0.193 14623 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramcarbohydrate.top
X-RAY DIFFRACTION3CNS_TOPPAR/ion.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4carbo_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION5cis_peptideT82Acova2009.paramCNS_TOPPAR/ion.top

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