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- PDB-8qy3: Xylanase from Bacillus circulans mutant E78Q/F125A bound to xylotriose -

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Basic information

Entry
Database: PDB / ID: 8qy3
TitleXylanase from Bacillus circulans mutant E78Q/F125A bound to xylotriose
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / BCX / glycosidase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETATE ION / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesNiallia circulans subsp. circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsChikunova, A. / Saberi, M. / Ubbink, M.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: Febs J. / Year: 2024
Title: Bimodal substrate binding in the active site of the glycosidase BcX.
Authors: Saberi, M. / Chikunova, A. / Ben Bdira, F. / Cramer-Blok, A. / Timmer, M. / Voskamp, P. / Ubbink, M.
History
DepositionOct 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2978
Polymers20,3321
Non-polymers9657
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.838, 80.838, 131.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11D-1-

XYP

21A-202-

ZN

31A-365-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Endo-1,4-beta-xylanase


Mass: 20331.924 Da / Num. of mol.: 1 / Mutation: E78Q, F125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Niallia circulans subsp. circulans (bacteria)
Gene: xlnA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09850
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 233 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acetate, 0.1 M BIS-TRIS, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.24→43.18 Å / Num. obs: 61224 / % possible obs: 99.1 % / Redundancy: 1.9 % / CC1/2: 0.998 / Net I/σ(I): 7.9
Reflection shellResolution: 1.24→1.26 Å / Num. unique obs: 2953 / CC1/2: 0.612

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→43.18 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.332 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22986 2991 5 %RANDOM
Rwork0.19541 ---
obs0.19709 56907 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.24→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 58 227 1727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0111605
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161369
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.6792201
X-RAY DIFFRACTIONr_angle_other_deg0.5611.593137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4535196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.25158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39610206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021987
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
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_it1.5861.916772
X-RAY DIFFRACTIONr_mcbond_other1.531.896769
X-RAY DIFFRACTIONr_mcangle_it2.0633.393970
X-RAY DIFFRACTIONr_mcangle_other2.0633.393971
X-RAY DIFFRACTIONr_scbond_it2.4712.216833
X-RAY DIFFRACTIONr_scbond_other2.4692.219834
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5353.9371232
X-RAY DIFFRACTIONr_long_range_B_refined10.74532.121922
X-RAY DIFFRACTIONr_long_range_B_other10.74632.121923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.24→1.271 Å
RfactorNum. reflection% reflection
Rfree1.695 225 -
Rwork1.623 4211 -
obs--98.1 %

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