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- PDB-3eyp: Crystal structure of putative alpha-L-fucosidase from Bacteroides... -

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Basic information

Entry
Database: PDB / ID: 3eyp
TitleCrystal structure of putative alpha-L-fucosidase from Bacteroides thetaiotaomicron
ComponentsPutative alpha-L-fucosidase
Keywordsstructural genomics / unknown function / HYDROLASE / Lipoprotein / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Hu, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative alpha-L-fucosidase from Bacteroides thetaiotaomicron
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Hu, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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 alpha-L-fucosidase
B: Putative alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,57310
Polymers106,8362
Non-polymers7378
Water11,494638
1
A: Putative alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7875
Polymers53,4181
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7875
Polymers53,4181
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.709, 125.193, 158.207
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 alpha-L-fucosidase / / Putative lipoprotein


Mass: 53418.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2192 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A5P6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 1.8M ammonium tri-citrate pH 7.0, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 15, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.9→98.173 Å / Num. all: 94178 / Num. obs: 94178 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.1 / Num. measured all: 137441 / Num. unique all: 13620 / Rsym value: 0.639 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.661 / WRfactor Rwork: 0.41 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.743 / SU B: 3.964 / SU ML: 0.113 / SU R Cruickshank DPI: 0.151 / SU Rfree: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4717 5 %RANDOM
Rwork0.208 ---
obs0.211 94091 99.99 %-
all-94100 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 79.62 Å2 / Biso mean: 46.17 Å2 / Biso min: 29.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2---0.6 Å20 Å2
3---2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7302 0 48 638 7988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227591
X-RAY DIFFRACTIONr_bond_other_d0.0010.025121
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.93810321
X-RAY DIFFRACTIONr_angle_other_deg1.826312417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59423.84362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.212151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9821543
X-RAY DIFFRACTIONr_chiral_restr0.1050.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218509
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021612
X-RAY DIFFRACTIONr_mcbond_it0.9011.54580
X-RAY DIFFRACTIONr_mcbond_other0.2791.51866
X-RAY DIFFRACTIONr_mcangle_it1.49127365
X-RAY DIFFRACTIONr_scbond_it2.57933011
X-RAY DIFFRACTIONr_scangle_it3.8784.52950
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 341 -
Rwork0.383 6490 -
all-6831 -
obs-6490 100 %

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