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- PDB-6yyh: Crystal structure of beta-D-xylosidase from Dictyoglomus thermoph... -

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Basic information

Entry
Database: PDB / ID: 6yyh
TitleCrystal structure of beta-D-xylosidase from Dictyoglomus thermophilum in ligand-free form
ComponentsBeta-xylosidase
KeywordsHYDROLASE / Carbohydrate
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / : / Glycosyl hydrolases family 39 / : / Glycoside hydrolase superfamily
Similarity search - Domain/homology
CITRIC ACID / Beta-xylosidase
Similarity search - Component
Biological speciesDictyoglomus thermophilum H-6-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsLafite, P. / Daniellou, R. / Bretagne, D.
CitationJournal: Biochimie / Year: 2020
Title: Crystal structure of Dictyoglomus thermophilum beta-d-xylosidase DtXyl unravels the structural determinants for efficient notoginsenoside R1 hydrolysis.
Authors: Bretagne, D. / Paris, A. / de Vaumas, R. / Lafite, P. / Daniellou, R.
History
DepositionMay 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: 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)122,8596
Polymers122,4132
Non-polymers4464
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-20 kcal/mol
Surface area40670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.140, 159.140, 100.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Beta-xylosidase


Mass: 61206.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum H-6-12 (bacteria)
Gene: DICTH_1792 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B5YB78, xylan 1,4-beta-xylosidase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Ammonium Sulfate 0.1 M Na citrate pH 5.6 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.72→47.06 Å / Num. obs: 39616 / % possible obs: 99.8 % / Redundancy: 20.886 % / Biso Wilson estimate: 72.964 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.11 / Χ2: 0.859 / Net I/σ(I): 23.69 / Num. measured all: 827425
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.72-2.8821.0741.2072.74131984633862630.8781.23798.8
2.88-3.0821.2370.7394.74126341595059490.9540.757100
3.08-3.3220.4970.3848.92113962556055600.9860.394100
3.32-3.6421.1030.216.96108408513751370.9960.205100
3.64-4.0721.4940.11828.17100269466546650.9980.12100
4.07-4.6920.3170.07641.3183788412441240.9990.078100
4.69-5.7320.8340.06547.4973314351935190.9990.067100
5.73-8.0421.0280.05753.6758017275927590.9990.059100
8.04-47.0619.1110.03185.07313421649164010.03299.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.56 Å47.06 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PX8

1px8


Resolution: 2.72→47.06 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.53
RfactorNum. reflection% reflection
Rfree0.2563 1979 5 %
Rwork0.1996 --
obs0.2024 39609 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.89 Å2 / Biso mean: 68.7327 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.72→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8298 0 27 35 8360
Biso mean--76.4 56.66 -
Num. residues----1002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.72-2.780.42071360.3272581271797
2.78-2.860.36321400.297726692809100
2.86-2.940.31831420.267626922834100
2.94-3.040.34081390.256326482787100
3.04-3.150.36311400.250926682808100
3.15-3.270.34311410.249426652806100
3.27-3.420.33461410.251826792820100
3.42-3.60.31071400.236526702810100
3.6-3.830.28631430.212427032846100
3.83-4.120.24511410.194826782819100
4.12-4.540.24741420.164727012843100
4.54-5.20.20441430.155827152858100
5.2-6.540.22411440.181127382882100
6.54-47.060.18231470.170928232970100

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