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- PDB-6i60: Structure of alpha-L-rhamnosidase from Dictyoglumus thermophilum -

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Basic information

Entry
Database: PDB / ID: 6i60
TitleStructure of alpha-L-rhamnosidase from Dictyoglumus thermophilum
ComponentsAlpha-rhamnosidase
KeywordsHYDROLASE / Glycoside hydrolase / Substrate
Function / homology
Function and homology information


alpha-L-rhamnosidase / alpha-L-rhamnosidase activity / carbohydrate metabolic process
Similarity search - Function
Alpha-L-rhamnosidase / Bacterial alpha-L-rhamnosidase N-terminal / Alpha-L-rhamnosidase N-terminal domain / Alpha-L-rhamnosidase, concanavalin-like domain / Bacterial alpha-L-rhamnosidase concanavalin-like domain / Alpha-L-rhamnosidase C-terminal domain / Bacterial alpha-L-rhamnosidase C-terminal domain / Alpha-L-rhamnosidase, six-hairpin glycosidase domain / Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain / Six-hairpin glycosidase-like superfamily ...Alpha-L-rhamnosidase / Bacterial alpha-L-rhamnosidase N-terminal / Alpha-L-rhamnosidase N-terminal domain / Alpha-L-rhamnosidase, concanavalin-like domain / Bacterial alpha-L-rhamnosidase concanavalin-like domain / Alpha-L-rhamnosidase C-terminal domain / Bacterial alpha-L-rhamnosidase C-terminal domain / Alpha-L-rhamnosidase, six-hairpin glycosidase domain / Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / TRIETHYLENE GLYCOL / Alpha-L-rhamnosidase
Similarity search - Component
Biological speciesDictyoglomus thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.743 Å
AuthorsLafite, P. / Daniellou, R.
CitationJournal: Acs Omega / Year: 2019
Title: Biochemical Characterization of the alpha-l-RhamnosidaseDtRha fromDictyoglomus thermophilum: Application to the Selective Derhamnosylation of Natural Flavonoids.
Authors: Guillotin, L. / Kim, H. / Traore, Y. / Moreau, P. / Lafite, P. / Coquoin, V. / Nuccio, S. / de Vaumas, R. / Daniellou, R.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 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: Alpha-rhamnosidase
B: Alpha-rhamnosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,46418
Polymers219,1422
Non-polymers2,32316
Water2,720151
1
A: Alpha-rhamnosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,04111
Polymers109,5711
Non-polymers1,47010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-rhamnosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4247
Polymers109,5711
Non-polymers8536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.220, 161.530, 124.380
Angle α, β, γ (deg.)90.000, 132.140, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-rhamnosidase


Mass: 109570.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12) (bacteria)
Strain: ATCC 35947 / DSM 3960 / H-6-12 / Gene: DICTH_0289 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5YC64
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.74→43.28 Å / Num. obs: 65285 / % possible obs: 97.9 % / Redundancy: 3.725 % / Biso Wilson estimate: 61.22 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.21 / Χ2: 0.955 / Net I/σ(I): 7.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.74-2.913.3940.9371.39101090.5031.11294.2
2.91-3.113.6490.5912.299700.7140.69299.2
3.11-3.363.7530.4433.5392660.8450.51798.9
3.36-3.683.8170.2815.8985530.9350.32698.9
3.68-4.113.8710.189.277390.9720.20898.7
4.11-4.743.9010.10913.968220.9890.12798.4
4.74-5.793.7920.1114.4357720.9850.12898.3
5.79-8.133.8380.08315.6945120.9920.09698.4
8.13-43.283.6560.05124.4725420.9960.0695.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5M

3w5m


Resolution: 2.743→43.28 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 30.73
RfactorNum. reflection% reflection
Rfree0.27 6330 4.99 %
Rwork0.2257 --
obs0.2279 63468 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.36 Å2 / Biso mean: 61.2588 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.743→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14488 0 150 151 14789
Biso mean--70.12 50.31 -
Num. residues----1769
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7432-2.77430.44761480.3872922307070
2.7743-2.8070.3962110.33153999421097
2.807-2.84120.3722100.34614025423597
2.8412-2.87710.43232110.35324015422697
2.8771-2.9150.35012110.35084052426397
2.915-2.95490.44352100.3294023423398
2.9549-2.99710.35372190.31254074429398
2.9971-3.04180.31042180.27714097431598
3.0418-3.08940.32732150.28924006422198
3.0894-3.140.34442110.28094094430598
3.14-3.19410.35952140.28584032424698
3.1941-3.25220.3142110.29124007421898
3.2522-3.31470.3692160.28734120433698
3.3147-3.38240.32092150.27974081429698
3.3824-3.45590.32412140.26453994420898
3.4559-3.53620.28342140.23674053426798
3.5362-3.62460.26722170.22964088430598
3.6246-3.72260.30132090.22264080428998
3.7226-3.8320.24562170.2174131434898
3.832-3.95560.25162150.21414069428498
3.9556-4.09690.24992110.20824068427999
4.0969-4.26080.25422160.19084074429098
4.2608-4.45450.20772110.184052426398
4.4545-4.68910.23962120.17684069428198
4.6891-4.98250.25932110.18724045425697
4.9825-5.36660.22562160.1924109432598
5.3666-5.90540.2222120.18534017422998
5.9054-6.75720.22642140.19554092430699
6.7572-8.50280.25712110.20144085429699
8.5028-43.2850.18612100.18493945415595

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