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- PDB-5ej3: Crystal structure of XlnB2 -

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Basic information

Entry
Database: PDB / ID: 5ej3
TitleCrystal structure of XlnB2
ComponentsEndo-1,4-beta-xylanase B
KeywordsHYDROLASE / xylanase B2 / xylan / beta-jelly roll domain / beta-glycosidase
Function / homology
Function and homology information


polysaccharide binding / endo-1,4-beta-xylanase / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region
Similarity search - Function
Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 ...Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / 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 / CBM2/CBM3, carbohydrate-binding domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase B
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.314 Å
AuthorsCouture, J.-F.
CitationJournal: Biochemistry / Year: 2016
Title: Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans.
Authors: Gagne, D. / Narayanan, C. / Nguyen-Thi, N. / Roux, L.D. / Bernard, D.N. / Brunzelle, J.S. / Couture, J.F. / Agarwal, P.K. / Doucet, N.
History
DepositionNov 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase B
B: Endo-1,4-beta-xylanase B


Theoretical massNumber of molelcules
Total (without water)51,1162
Polymers51,1162
Non-polymers00
Water7,386410
1
A: Endo-1,4-beta-xylanase B


Theoretical massNumber of molelcules
Total (without water)25,5581
Polymers25,5581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase B


Theoretical massNumber of molelcules
Total (without water)25,5581
Polymers25,5581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.097, 66.941, 65.483
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-1,4-beta-xylanase B / Xylanase B / 1 / 4-beta-D-xylan xylanohydrolase B


Mass: 25558.182 Da / Num. of mol.: 2 / Fragment: UNP residues 1-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: xlnB / Production host: Streptomyces lividans (bacteria) / References: UniProt: P26515, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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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: 1.76 Å3/Da / Density % sol: 30.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M zinc acetate dehydrate, 0.1 M sodium acetate pH 4.5 and 10 % w/v PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→46.749 Å / Num. obs: 81872 / % possible obs: 96.4 % / Redundancy: 4.2 % / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.314→46.749 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1668 3914 4.78 %
Rwork0.1295 --
obs0.1313 81872 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.314→46.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 0 410 3365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143160
X-RAY DIFFRACTIONf_angle_d1.4234335
X-RAY DIFFRACTIONf_dihedral_angle_d11.0031117
X-RAY DIFFRACTIONf_chiral_restr0.078443
X-RAY DIFFRACTIONf_plane_restr0.01564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3141-1.33010.24321570.19232708X-RAY DIFFRACTION95
1.3301-1.3470.25351370.19082692X-RAY DIFFRACTION96
1.347-1.36470.22771280.1772783X-RAY DIFFRACTION96
1.3647-1.38340.22121470.17252708X-RAY DIFFRACTION97
1.3834-1.40320.22731330.15792765X-RAY DIFFRACTION96
1.4032-1.42410.21051760.15622727X-RAY DIFFRACTION96
1.4241-1.44640.19371410.14942736X-RAY DIFFRACTION97
1.4464-1.47010.2161400.15062735X-RAY DIFFRACTION96
1.4701-1.49540.20721450.14122775X-RAY DIFFRACTION98
1.4954-1.52260.18191190.13212792X-RAY DIFFRACTION96
1.5226-1.55190.16721430.12332764X-RAY DIFFRACTION98
1.5519-1.58360.16021550.11852763X-RAY DIFFRACTION96
1.5836-1.6180.18391330.11982783X-RAY DIFFRACTION99
1.618-1.65570.19321340.12172795X-RAY DIFFRACTION97
1.6557-1.69710.1551360.12092793X-RAY DIFFRACTION98
1.6971-1.74290.19351320.12072814X-RAY DIFFRACTION98
1.7429-1.79420.16581340.11882805X-RAY DIFFRACTION97
1.7942-1.85210.1641320.11612808X-RAY DIFFRACTION99
1.8521-1.91830.1891170.11352852X-RAY DIFFRACTION98
1.9183-1.99520.15241370.11422805X-RAY DIFFRACTION98
1.9952-2.0860.15421330.11842803X-RAY DIFFRACTION98
2.086-2.19590.13421080.11562824X-RAY DIFFRACTION98
2.1959-2.33350.15071590.12152828X-RAY DIFFRACTION98
2.3335-2.51370.17311480.13552807X-RAY DIFFRACTION98
2.5137-2.76660.17281360.14092831X-RAY DIFFRACTION98
2.7666-3.16690.1651420.13042819X-RAY DIFFRACTION98
3.1669-3.98960.13121420.1192807X-RAY DIFFRACTION97
3.9896-46.77850.15441700.13222836X-RAY DIFFRACTION97

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