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- PDB-4ozo: Crystal structure of an a-L-fucosidase GH29 from Bacteroides thet... -

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Basic information

Entry
Database: PDB / ID: 4ozo
TitleCrystal structure of an a-L-fucosidase GH29 from Bacteroides thetaiotaomicron (BT2192) in complex with oNPTG
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
2-nitrophenyl 1-thio-beta-D-galactopyranoside / Lipoprotein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLafite, P. / Daniellou, R. / Guillotin, L.
Funding support France, 1items
OrganizationGrant numberCountry
R?gion Centre France
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 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software / struct_keywords / struct_site
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text / _struct_site.details
Revision 1.4Jul 29, 2020Group: Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Putative lipoprotein
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8398
Polymers106,8362
Non-polymers1,0036
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-5 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.300, 122.170, 159.650
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-OTN / 2-nitrophenyl 1-thio-beta-D-galactopyranoside / (2R,3R,4S,5R,6S)-2-(hydroxymethyl)-6-(2-nitrophenyl)sulfanyl-oxane-3,4,5-triol / 2-nitrophenyl 1-thio-beta-D-galactoside / 2-nitrophenyl 1-thio-D-galactoside / 2-nitrophenyl 1-thio-galactoside


Type: D-saccharide / Mass: 317.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5 M ammonium citrate, soaking with 250 mM ligand

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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 / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→49 Å / Num. obs: 38008 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 37.8 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.138 / Χ2: 1.013 / Net I/σ(I): 13.76 / Num. measured all: 281551
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.6-2.70.9050.6623.5930000403740340.71399.9
2.7-70.9960.12913.8523734031902318990.138100
70.9990.04132.1214211208520750.04499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYP

3eyp


Resolution: 2.6→49 Å / FOM work R set: 0.8454 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 1901 5 %
Rwork0.1653 36096 -
obs0.1681 37997 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.95 Å2 / Biso mean: 18.65 Å2 / Biso min: 3.61 Å2
Refinement stepCycle: final / Resolution: 2.6→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7300 0 66 203 7569
Biso mean--23.37 19.13 -
Num. residues----918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077570
X-RAY DIFFRACTIONf_angle_d1.07210294
X-RAY DIFFRACTIONf_chiral_restr0.071088
X-RAY DIFFRACTIONf_plane_restr0.0041320
X-RAY DIFFRACTIONf_dihedral_angle_d13.7172714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.6650.2781340.211125382672
2.665-2.7370.25691340.187225432677
2.737-2.81760.24961350.179325692704
2.8176-2.90850.25591340.165225402674
2.9085-3.01240.20561330.166425362669
3.0124-3.1330.24531360.161425812717
3.133-3.27560.24391340.159425512685
3.2756-3.44820.22681350.156125512686
3.4482-3.66420.20041350.140525702705
3.6642-3.9470.19021360.147925932729
3.947-4.3440.18181360.145225762712
4.344-4.97210.2151370.16325982735
4.9721-6.26230.2091380.187726252763
6.2623-490.24281440.184627252869

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