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- PDB-6ife: A Glycoside Hydrolase Family 43 beta-Xylosidase -

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Basic information

Entry
Database: PDB / ID: 6ife
TitleA Glycoside Hydrolase Family 43 beta-Xylosidase
ComponentsBeta-xylosidaseXylan 1,4-b-xylosidase
KeywordsHYDROLASE / Glycoside Hydrolase Family 43 / beta-Xylosidase / Low-temperature Activity / Salt Tolerance
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / carbohydrate metabolic 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: 1.804 Å
AuthorsLi, N. / Liu, Y. / Zhang, R. / Zhou, J.P. / Huang, Z.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31660445 China
CitationJournal: Food Chem / Year: 2019
Title: Biochemical and structural properties of a low-temperature-active glycoside hydrolase family 43 beta-xylosidase: Activity and instability at high neutral salt concentrations.
Authors: Zhang, R. / Li, N. / Liu, Y. / Han, X. / Tu, T. / Shen, J. / Xu, S. / Wu, Q. / Zhou, J. / Huang, Z.
History
DepositionSep 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _struct_ref.db_code ..._entity_src_gen.gene_src_common_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.3Nov 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)127,6697
Polymers127,2082
Non-polymers4605
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-14 kcal/mol
Surface area37150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.637, 106.135, 105.884
Angle α, β, γ (deg.)90.00, 122.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-xylosidase / Xylan 1,4-b-xylosidase


Mass: 63604.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: B4107_1875 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A4V8GZZ0, xylan 1,4-beta-xylosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGB KY391885 Authors state that the Genebank accession number is KY391885 for this sequence.

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH=8.5, 30% PEG4000, 0.2 M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→89.29 Å / Num. obs: 74733 / % possible obs: 70.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.06 / Net I/av σ(I): 14.3 / Net I/σ(I): 14.3
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7222 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIF

1yif


Resolution: 1.804→40.24 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.13
RfactorNum. reflection% reflection
Rfree0.1991 1921 2.67 %
Rwork0.1608 --
obs0.1618 71870 67.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.804→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8633 0 30 448 9111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078932
X-RAY DIFFRACTIONf_angle_d1.01912146
X-RAY DIFFRACTIONf_dihedral_angle_d4.4755167
X-RAY DIFFRACTIONf_chiral_restr0.061265
X-RAY DIFFRACTIONf_plane_restr0.0071567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8036-1.84870.29661450.23465343X-RAY DIFFRACTION90
1.9546-2.01770.2681440.19054837X-RAY DIFFRACTION94
2.0177-2.08980.163480.20371969X-RAY DIFFRACTION87
2.0898-2.17350.23811680.19726120X-RAY DIFFRACTION91
2.1735-2.27240.2958740.22562467X-RAY DIFFRACTION75
2.2724-2.39220.21781930.18026990X-RAY DIFFRACTION96
2.3922-2.5420.26332050.18177200X-RAY DIFFRACTION98
2.542-2.73830.21581860.18557063X-RAY DIFFRACTION96
2.7383-3.01370.21251870.18177144X-RAY DIFFRACTION96
3.0137-3.44960.21950.16446926X-RAY DIFFRACTION94
3.4496-4.34530.16891880.12756857X-RAY DIFFRACTION93
4.3453-40.25020.14661880.12987033X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 58.5432 Å / Origin y: -58.1056 Å / Origin z: 110.5125 Å
111213212223313233
T0.0654 Å2-0.009 Å20.0194 Å2-0.1145 Å20.0054 Å2--0.0873 Å2
L0.1392 °20.0328 °20.0765 °2-0.4699 °2-0.0525 °2--0.487 °2
S-0.0007 Å °-0.0268 Å °0.0021 Å °0.0528 Å °0.0063 Å °0.0382 Å °0.0007 Å °-0.0918 Å °0.0036 Å °
Refinement TLS groupSelection details: all

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