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- PDB-8r86: Xylanase from Bacillus circulans mutant E78Q/W71A -

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Basic information

Entry
Database: PDB / ID: 8r86
TitleXylanase from Bacillus circulans mutant E78Q/W71A
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: 1.5 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
DepositionNov 28, 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.page_last

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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
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)40,5862
Polymers40,5862
Non-polymers00
Water9,296516
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,2931
Polymers20,2931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,2931
Polymers20,2931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.787, 39.899, 53.653
Angle α, β, γ (deg.)85.26, 81.43, 63.26
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 20292.889 Da / Num. of mol.: 2 / Mutation: E78Q, W71A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O
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: 1.85 Å3/Da / Density % sol: 33.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20.727 %v/v PEGSH, 0.1 M BICINE 8.81 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.5→27.81 Å / Num. obs: 42397 / % possible obs: 90.6 % / Redundancy: 1.5 % / CC1/2: 0.986 / Net I/σ(I): 9.8
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2153 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→27.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.208 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17302 2044 4.8 %RANDOM
Rwork0.13733 ---
obs0.13898 40351 90.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.485 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.15 Å20.04 Å2
2--0.03 Å20.08 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.5→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 0 516 3394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0113119
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162515
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6524302
X-RAY DIFFRACTIONr_angle_other_deg0.541.5545867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4065403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.9515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11910415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
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_it0.6740.6211567
X-RAY DIFFRACTIONr_mcbond_other0.6740.6211567
X-RAY DIFFRACTIONr_mcangle_it1.0730.931985
X-RAY DIFFRACTIONr_mcangle_other1.0720.931986
X-RAY DIFFRACTIONr_scbond_it1.1230.6961552
X-RAY DIFFRACTIONr_scbond_other1.1230.6961553
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6791.0142318
X-RAY DIFFRACTIONr_long_range_B_refined4.0819.5383799
X-RAY DIFFRACTIONr_long_range_B_other3.71312.1813631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 159 -
Rwork0.147 3021 -
obs--91.7 %

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