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- PDB-4oue: Crystal structure of an a-L-Fucosidase GH29 from Bacteroides thet... -

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Basic information

Entry
Database: PDB / ID: 4oue
TitleCrystal structure of an a-L-Fucosidase GH29 from Bacteroides thetaiotaomicron (BT2192) in complex with IPTG
ComponentsPutative lipoprotein
KeywordsHYDROLASE / beta sandwich / glycosyl hydrolase GH29
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls ...Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1-methylethyl 1-thio-beta-D-galactopyranoside / Lipoprotein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsLafite, P. / Daniellou, R. / Guillotin, L.
CitationJournal: Biochemistry / Year: 2014
Title: Unraveling the Substrate Recognition Mechanism and Specificity of the Unusual Glycosyl Hydrolase Family 29 BT2192 from Bacteroides thetaiotaomicron.
Authors: Guillotin, L. / Lafite, P. / Daniellou, R.
History
DepositionFeb 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references / Structure summary
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: Putative lipoprotein
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6818
Polymers106,8362
Non-polymers8456
Water7,494416
1
A: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8414
Polymers53,4181
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8414
Polymers53,4181
Non-polymers4223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.680, 122.080, 159.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Putative lipoprotein / Alpha-L-fucosidase


Mass: 53418.172 Da / Num. of mol.: 2 / Fragment: UNP residues 26-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2192 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q8A5P6, EC: 3.2.1.111
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-IPT / 1-methylethyl 1-thio-beta-D-galactopyranoside / ISOPROPYL-1-BETA-D-THIOGALACTOSIDE / 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE / 1-methylethyl 1-thio-beta-D-galactoside / 1-methylethyl 1-thio-D-galactoside / 1-methylethyl 1-thio-galactoside


Type: D-saccharide / Mass: 238.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18O5S
IdentifierTypeProgram
isopropyl-1-b-D-thiogalactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5 M ammonium citrate, soaking with 250 mM ligand, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→49.5 Å / Num. obs: 51368 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.98 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.021 / Net I/σ(I): 17.72
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.35-2.450.5844.434491559631100
2.45-100.09119.1332200446611100
10-49.50.03241.384799744198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→48.997 Å / FOM work R set: 0.8811 / SU ML: 0.16 / σ(F): 2 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 2566 5 %RANDOM
Rwork0.1551 ---
obs0.1572 51353 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.26 Å2 / Biso mean: 22.87 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: LAST / Resolution: 2.35→48.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 54 416 7778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077576
X-RAY DIFFRACTIONf_angle_d1.01810299
X-RAY DIFFRACTIONf_chiral_restr0.0691089
X-RAY DIFFRACTIONf_plane_restr0.0041319
X-RAY DIFFRACTIONf_dihedral_angle_d13.9322713
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3501-2.39530.21791410.163326682809
2.3953-2.44410.22391400.169226712811
2.4441-2.49730.24851420.161627102852
2.4973-2.55540.2041400.161126582798
2.5554-2.61930.23521420.160827032845
2.6193-2.69010.21321410.154126772818
2.6901-2.76920.22241410.149626882829
2.7692-2.85860.2041420.149826792821
2.8586-2.96080.22391430.147327172860
2.9608-3.07930.21951410.149226822823
3.0793-3.21940.22291420.134227022844
3.2194-3.38910.15641420.140927282870
3.3891-3.60140.17181420.129626902832
3.6014-3.87940.18031430.13227112854
3.8794-4.26950.18451430.143327252868
4.2695-4.88690.18981450.153227472892
4.8869-6.1550.17831450.182327582903
6.155-49.00740.21281510.199128733024

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