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- PDB-8qy2: Xylanase from Bacillus circulans mutant E78Q/F125A -

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Basic information

Entry
Database: PDB / ID: 8qy2
TitleXylanase from Bacillus circulans mutant E78Q/F125A
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE
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
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesNiallia circulans subsp. circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)20,9487
Polymers20,3321
Non-polymers6166
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.714, 78.714, 131.998
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
11A-205-

ZN

21A-336-

HOH

31A-404-

HOH

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Components

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 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: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→42.58 Å / Num. obs: 23035 / % possible obs: 99.4 % / Redundancy: 1.9 % / CC1/2: 0.999 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1149 / CC1/2: 0.655

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.58 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.231 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 1091 4.8 %RANDOM
Rwork0.19053 ---
obs0.19164 21750 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.918 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å2-0 Å2
2--0.63 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: 1 / Resolution: 1.7→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 34 127 1603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0111534
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161304
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.6762101
X-RAY DIFFRACTIONr_angle_other_deg0.5061.592982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7335188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.27457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67410196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
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_it1.6182.099749
X-RAY DIFFRACTIONr_mcbond_other1.6182.099749
X-RAY DIFFRACTIONr_mcangle_it1.9983.754938
X-RAY DIFFRACTIONr_mcangle_other1.9993.754939
X-RAY DIFFRACTIONr_scbond_it2.8192.37785
X-RAY DIFFRACTIONr_scbond_other2.8172.369786
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.034.2151164
X-RAY DIFFRACTIONr_long_range_B_refined6.08523.951735
X-RAY DIFFRACTIONr_long_range_B_other6.06623.491715
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree1.026 84 -
Rwork1.011 1327 -
obs--83.39 %

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