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

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Basic information

Entry
Database: PDB / ID: 6yyi
TitleCrystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to beta-D-xylopyranose
ComponentsBeta-xylosidase
KeywordsHYDROLASE / Carbohydrate Substrate complex
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-D-xylopyranose / Beta-xylosidase
Similarity search - Component
Biological speciesDictyoglomus thermophilum H-6-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.67 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)123,73820
Polymers122,4132
Non-polymers1,32518
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-19 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.950, 160.950, 103.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#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 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B5YB78, xylan 1,4-beta-xylosidase
#5: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-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

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Non-polymers , 5 types, 92 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Ammonium sulfate 10% PEG 4000 0,1M Sodium citrate pH 5.6

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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: 2.67→48.57 Å / Num. obs: 43883 / % possible obs: 99.8 % / Redundancy: 20.765 % / Biso Wilson estimate: 53.801 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.172 / Rrim(I) all: 0.176 / Χ2: 0.835 / Net I/σ(I): 17.17 / Num. measured all: 911219
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
2.67-2.8420.2851.1382.71140189700669110.8921.16798.6
2.84-3.0320.4820.7664.21135675662466240.9520.785100
3.03-3.2721.0530.4587.16129773616461640.9840.469100
3.27-3.5821.6430.2612.94123213569356930.9940.266100
3.58-421.0730.15820.52108506515051490.9980.162100
4-4.6220.0830.10829.3291900457645760.9980.11100
4.62-5.6421.4070.09334.0483508390139010.9990.095100
5.64-7.9320.5180.09233.8262930306730670.9990.095100
7.93-48.5719.7580.04362.62355251807179810.04499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.64 Å48.57 Å
Translation6.64 Å48.57 Å

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Processing

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

1px8


Resolution: 2.67→48.57 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.63
RfactorNum. reflection% reflection
Rfree0.2271 2192 5 %
Rwork0.1774 --
obs0.1799 43866 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.68 Å2 / Biso mean: 53.4438 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.67→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8322 0 83 75 8480
Biso mean--60.93 46.88 -
Num. residues----1004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.730.31431330.28162516264997
2.73-2.80.34681340.246725432677100
2.8-2.870.33841360.244525902726100
2.87-2.940.30241380.238726132751100
2.94-3.030.30611340.233925612695100
3.03-3.130.31461370.232126022739100
3.13-3.240.26571370.211225982735100
3.24-3.370.28911360.204325762712100
3.37-3.520.26971360.205425872723100
3.52-3.710.24221370.19626072744100
3.71-3.940.23481370.164626042741100
3.94-4.250.18691370.155326192756100
4.25-4.670.17581380.125626252763100
4.67-5.350.17191390.135126312770100
5.35-6.730.20111400.162626542794100
6.74-48.570.17231430.157127482891100

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