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- PDB-6wqw: Thermobacillus composti GH10 xylanase -

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Basic information

Entry
Database: PDB / ID: 6wqw
TitleThermobacillus composti GH10 xylanase
ComponentsBeta-xylanaseXylanase
KeywordsHYDROLASE / GH 10 / Glycoside Hydrolase / Thermobacillus composti
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-D-xylopyranose / Beta-xylanase
Similarity search - Component
Biological speciesThermobacillus composti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 Å
AuthorsBriganti, L. / Polikarpov, I.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)423693/2016-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303988/2016-9 Brazil
Sao Paulo Research Foundation (FAPESP)2015/13684-0 Brazil
CitationJournal: Carbohydr Polym / Year: 2020
Title: Transformation of xylan into value-added biocommodities using Thermobacillus composti GH10 xylanase.
Authors: Sepulchro, A.G.V. / Pellegrini, V.O.A. / Briganti, L. / de Araujo, E.A. / de Araujo, S.S. / Polikarpov, I.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7452
Polymers38,5941
Non-polymers1501
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.264, 81.264, 92.363
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Beta-xylanase / Xylanase


Mass: 38594.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobacillus composti (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: L0EGW1, endo-1,4-beta-xylanase
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 70% (v/v) 2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.102→33.82 Å / Num. obs: 18595 / % possible obs: 98.4 % / Redundancy: 22.7 % / CC1/2: 1 / Net I/σ(I): 18.26
Reflection shellResolution: 2.102→2.18 Å / Redundancy: 19.4 % / Mean I/σ(I) obs: 2.23 / Num. unique obs: 1809 / CC1/2: 0.868 / % possible all: 99.78

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.73 Å40.16 Å
Translation5.73 Å40.16 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N82

1n82


Resolution: 2.102→33.819 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 919 5.02 %
Rwork0.2347 17388 -
obs0.2364 18307 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.23 Å2 / Biso mean: 48.2512 Å2 / Biso min: 16.26 Å2
Refinement stepCycle: final / Resolution: 2.102→33.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 10 106 2630
Biso mean--54.99 39.83 -
Num. residues----305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.102-2.21270.36551250.31332461100
2.2127-2.35130.31781300.28572458100
2.3513-2.53270.31181300.27882495100
2.5327-2.78750.2941510.25032474100
2.7875-3.19060.23551220.2378248199
3.1906-4.01880.23841180.2078246096
4.0188-33.8190.2591430.2212255995
Refinement TLS params.Method: refined / Origin x: 54.044 Å / Origin y: 25.2786 Å / Origin z: 47.0567 Å
111213212223313233
T0.2312 Å20.0224 Å2-0.0246 Å2-0.2209 Å2-0.0103 Å2--0.2721 Å2
L1.6494 °20.2857 °2-1.0833 °2-1.5585 °2-0.3251 °2--3.957 °2
S0.1503 Å °-0.0908 Å °0.0286 Å °0.0789 Å °-0.0968 Å °-0.1425 Å °-0.1993 Å °0.1152 Å °0.0162 Å °
Refinement TLS groupSelection details: (chain A and resseq 4:330)

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