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- PDB-5i5r: Crystal structure of a bacterial fucosidase with iminocyclitol (2... -

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Basic information

Entry
Database: PDB / ID: 5i5r
TitleCrystal structure of a bacterial fucosidase with iminocyclitol (2S,3S,4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / enzyme inhibition
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Alpha-L-fucosidase, metazoa-type / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Alpha-L-fucosidase, metazoa-type / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-68F / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWright, D.W. / Davies, G.J.
CitationJournal: To Be Published
Title: Will be disclosed later
Authors: Behr, J.B. / Wright, D.W. / Hottin, A. / Moreno-Vargas, A.J. / Robina, I. / Davies, G.J.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,57620
Polymers206,3784
Non-polymers2,19816
Water13,926773
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1445
Polymers51,5941
Non-polymers5504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2406
Polymers51,5941
Non-polymers6465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1445
Polymers51,5941
Non-polymers5504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0484
Polymers51,5941
Non-polymers4543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.080, 187.699, 97.640
Angle α, β, γ (deg.)90.000, 94.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA35 - 4792 - 446
21TYRTYRBB35 - 4792 - 446
12LYSLYSAA35 - 4732 - 440
22LYSLYSCC35 - 4732 - 440
13TYRTYRAA35 - 4792 - 446
23TYRTYRDD35 - 4792 - 446
14LYSLYSBB35 - 4732 - 440
24LYSLYSCC35 - 4732 - 440
15TYRTYRBB35 - 4792 - 446
25TYRTYRDD35 - 4792 - 446
16LYSLYSCC35 - 4732 - 440
26LYSLYSDD35 - 4732 - 440

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alpha-L-fucosidase


Mass: 51594.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Gene: BT_2970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A3I4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-68F / (2S,3S,4R,5S,2'S,3'S,4'R,5'S)-2,2'-(butane-1,4-diyl)bis(5-methylpyrrolidine-3,4-diol)


Mass: 288.383 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% w/v PEG 3350, 0.1 M ammonium sulfate, 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→67.57 Å / Num. obs: 116721 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.143.90.891199.8
11.5-67.573.80.047199.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.2.17data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MNZ

1mnz


Resolution: 2.1→67.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.564 / SU ML: 0.163 / SU R Cruickshank DPI: 0.2288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.187
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 5869 5 %RANDOM
Rwork0.1951 ---
obs0.1971 110778 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.73 Å2 / Biso mean: 44.105 Å2 / Biso min: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å2-1.15 Å2
2--0.17 Å20 Å2
3----2.2 Å2
Refinement stepCycle: final / Resolution: 2.1→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14201 0 140 773 15114
Biso mean--62.34 43.37 -
Num. residues----1761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214779
X-RAY DIFFRACTIONr_bond_other_d0.0080.0213427
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.93620087
X-RAY DIFFRACTIONr_angle_other_deg1.3193.00430908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79351759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43123.986705
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.116152361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1491574
X-RAY DIFFRACTIONr_chiral_restr0.0930.22064
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116660
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023550
X-RAY DIFFRACTIONr_mcbond_it3.6814.2617042
X-RAY DIFFRACTIONr_mcbond_other3.6794.2617041
X-RAY DIFFRACTIONr_mcangle_it5.0856.3798790
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A539280.06
12B539280.06
21A529640.06
22C529640.06
31A535060.05
32D535060.05
41B542880.05
42C542880.05
51B546040.05
52D546040.05
61C541400.06
62D541400.06
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 425 -
Rwork0.307 8199 -
all-8624 -
obs--99.53 %

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