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- PDB-5xzu: Crystal structure of GH10 xylanase from Bispora. sp MEY-1 with xy... -

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Basic information

Entry
Database: PDB / ID: 5xzu
TitleCrystal structure of GH10 xylanase from Bispora. sp MEY-1 with xylobiose
ComponentsBeta-xylanase
KeywordsHYDROLASE / GH10 family / xylanase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / Beta-xylanase
Similarity search - Component
Biological speciesBispora sp. MEY-1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsYou, S. / Chen, C.C. / Tu, T. / Guo, R.T. / Luo, H.Y. / Yao, B.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31472127 China
CitationJournal: Biotechnol Biofuels / Year: 2018
Title: Insight into the functional roles of Glu175 in the hyperthermostable xylanase XYL10C-Delta N through structural analysis and site-saturation mutagenesis.
Authors: You, S. / Chen, C.C. / Tu, T. / Wang, X. / Ma, R. / Cai, H.Y. / Guo, R.T. / Luo, H.Y. / Yao, B.
History
DepositionJul 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_close_contact / 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 / _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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6918
Polymers75,2432
Non-polymers1,4486
Water10,935607
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint4 kcal/mol
Surface area25550 Å2
Unit cell
Length a, b, c (Å)135.274, 83.136, 65.387
Angle α, β, γ (deg.)90.00, 94.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-524-

HOH

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Components

#1: Protein Beta-xylanase


Mass: 37621.500 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bispora sp. MEY-1 (fungus) / Gene: xyl10C / Production host: Komagataella pastoris GS115 (fungus) / Strain (production host): GS115 / References: UniProt: D0QF43, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][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.: 5
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 19% PEG 3350, 0.4 M magnesium chloride, 0.1 M BIS-TRIS HYDROCHLORIDE pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1.00919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00919 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 79182 / % possible obs: 99.9 % / Redundancy: 4.2 % / Net I/σ(I): 5.96

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.973 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18323 4011 5.1 %RANDOM
Rwork0.12376 ---
obs0.12691 75179 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.035 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å22.2 Å2
2---0.72 Å20 Å2
3---1.89 Å2
Refinement stepCycle: 1 / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5286 0 93 608 5987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025539
X-RAY DIFFRACTIONr_bond_other_d0.0010.024899
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9387578
X-RAY DIFFRACTIONr_angle_other_deg0.811311284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7875665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68125.484279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82715800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2971512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.026375
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021317
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_it4.1263.0062666
X-RAY DIFFRACTIONr_mcbond_other4.1233.0052665
X-RAY DIFFRACTIONr_mcangle_it4.4884.53329
X-RAY DIFFRACTIONr_mcangle_other4.4884.53330
X-RAY DIFFRACTIONr_scbond_it6.333.4262872
X-RAY DIFFRACTIONr_scbond_other6.333.4262872
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7734.9984250
X-RAY DIFFRACTIONr_long_range_B_refined5.71537.4716569
X-RAY DIFFRACTIONr_long_range_B_other5.65337.0096455
X-RAY DIFFRACTIONr_rigid_bond_restr6.349310436
X-RAY DIFFRACTIONr_sphericity_free23.555439
X-RAY DIFFRACTIONr_sphericity_bonded14.046510447
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 283 -
Rwork0.17 5561 -
obs--99.97 %

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