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- PDB-5zqj: Crystal structure of beta-xylosidase from Bacillus pumilus -

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Basic information

Entry
Database: PDB / ID: 5zqj
TitleCrystal structure of beta-xylosidase from Bacillus pumilus
ComponentsBeta-xylosidase
KeywordsHYDROLASE / xylobiose hydrolysis
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process
Similarity search - Function
Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsHa, N.C. / Hong, S. / Jo, I.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structure-based protein engineering of bacterial beta-xylosidase to increase the production yield of xylobiose from xylose
Authors: Hong, S. / Kyung, M. / Jo, I. / Kim, Y.R. / Ha, N.C.
History
DepositionApr 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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-xylosidase
B: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7348
Polymers124,1812
Non-polymers5536
Water16,880937
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, homodimer state (68% (w/w))
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-13 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.261, 105.201, 105.814
Angle α, β, γ (deg.)90.00, 122.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-xylosidase / 1 / 4-beta-D-xylan xylohydrolase / Xylan 1 / 4-beta-xylosidase


Mass: 62090.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: xynB / Production host: Escherichia coli (E. coli) / References: UniProt: P07129, xylan 1,4-beta-xylosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.05M HEPES (pH 7.5), 20%(w/v) PEG 3350, 1%(w/v) tryptone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 107503 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.036 / Rrim(I) all: 0.088 / Χ2: 0.992 / Net I/σ(I): 17.23
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 5058 / CC1/2: 0.785 / Rpim(I) all: 0.18 / Rrim(I) all: 0.347 / Χ2: 0.767 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIF

1yif


Resolution: 1.73→47.245 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 17.83
RfactorNum. reflection% reflection
Rfree0.1882 4934 4.99 %
Rwork0.1545 --
obs0.1562 98865 89.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→47.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8654 0 36 937 9627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078956
X-RAY DIFFRACTIONf_angle_d0.87512172
X-RAY DIFFRACTIONf_dihedral_angle_d3.565214
X-RAY DIFFRACTIONf_chiral_restr0.0561263
X-RAY DIFFRACTIONf_plane_restr0.0061571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7304-1.750.2487720.21231638X-RAY DIFFRACTION47
1.75-1.77060.25611110.19651856X-RAY DIFFRACTION53
1.7706-1.79220.23581080.19242033X-RAY DIFFRACTION59
1.7922-1.81490.20831330.20032205X-RAY DIFFRACTION63
1.8149-1.83880.22521610.20072311X-RAY DIFFRACTION68
1.8388-1.8640.23571450.20442540X-RAY DIFFRACTION73
1.864-1.89060.26071600.19292776X-RAY DIFFRACTION80
1.8906-1.91880.24071600.18712985X-RAY DIFFRACTION86
1.9188-1.94880.21361430.19063212X-RAY DIFFRACTION90
1.9488-1.98080.21221900.17453205X-RAY DIFFRACTION93
1.9808-2.01490.20292140.17633266X-RAY DIFFRACTION95
2.0149-2.05160.21021710.17443383X-RAY DIFFRACTION96
2.0516-2.0910.17811420.17693391X-RAY DIFFRACTION97
2.091-2.13370.24081730.17023398X-RAY DIFFRACTION97
2.1337-2.18010.23061960.16373426X-RAY DIFFRACTION98
2.1801-2.23080.21482000.16253396X-RAY DIFFRACTION97
2.2308-2.28660.19321840.15463434X-RAY DIFFRACTION98
2.2866-2.34840.19252020.15183443X-RAY DIFFRACTION99
2.3484-2.41750.19721550.16133450X-RAY DIFFRACTION99
2.4175-2.49560.19981890.15793460X-RAY DIFFRACTION99
2.4956-2.58470.19581580.15643523X-RAY DIFFRACTION99
2.5847-2.68820.21671630.15633479X-RAY DIFFRACTION99
2.6882-2.81060.19911840.16013481X-RAY DIFFRACTION99
2.8106-2.95870.20561690.15543478X-RAY DIFFRACTION99
2.9587-3.14410.18321760.15433490X-RAY DIFFRACTION100
3.1441-3.38670.18861540.14763535X-RAY DIFFRACTION100
3.3867-3.72740.16351690.13743529X-RAY DIFFRACTION100
3.7274-4.26650.14521870.12353492X-RAY DIFFRACTION100
4.2665-5.37420.13111920.12093515X-RAY DIFFRACTION100
5.3742-47.26290.16891730.15333601X-RAY DIFFRACTION100

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