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

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Basic information

Entry
Database: PDB / ID: 5hdr
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 / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / 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 / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / 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-H79 / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsWright, D.W. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S,4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine
Authors: Wright, D.W. / Davies, G.J.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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)209,36017
Polymers207,0064
Non-polymers2,35313
Water8,017445
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4125
Polymers51,7521
Non-polymers6604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4125
Polymers51,7521
Non-polymers6604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3164
Polymers51,7521
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2203
Polymers51,7521
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.500, 188.760, 98.140
Angle α, β, γ (deg.)90.000, 93.890, 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: 51751.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2970 / Plasmid: YSBLIC3C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A3I4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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-H79 / [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-1-{3-[4-(3,4-dihydroxy-5-methylpyrrolidin-2-yl)-1H-1,2,3-triazol-1-yl]prop-1-en-1-yl}cyclopentadienyl]iron


Mass: 399.204 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H15FeN4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.1 M ammonium sulfate, 0.1 M imidazole
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 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: 2.3→67.95 Å / Num. obs: 90452 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.069 / Net I/σ(I): 5.9 / Num. measured all: 330229 / Scaling rejects: 39
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.343.71.0231.21673845270.5610.61699.7
12.6-67.953.60.04616.920885810.9870.02999.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.14data extraction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2WVV

2wvv


Resolution: 2.3→97.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.858 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.351 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 4558 5.1 %RANDOM
Rwork0.2012 ---
obs0.2033 85655 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.18 Å2 / Biso mean: 52.52 Å2 / Biso min: 22.45 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å2-0 Å2-0.68 Å2
2---0.07 Å20 Å2
3----4.31 Å2
Refinement stepCycle: final / Resolution: 2.3→97.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14144 0 153 445 14742
Biso mean--108.01 44.31 -
Num. residues----1761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214779
X-RAY DIFFRACTIONr_bond_other_d0.0070.0213280
X-RAY DIFFRACTIONr_angle_refined_deg2.4261.9520300
X-RAY DIFFRACTIONr_angle_other_deg1.555330556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52751759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67624.026703
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.653152314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.621572
X-RAY DIFFRACTIONr_chiral_restr0.1060.22082
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116698
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023562
X-RAY DIFFRACTIONr_mcbond_it3.8825.1047042
X-RAY DIFFRACTIONr_mcbond_other3.8825.1047041
X-RAY DIFFRACTIONr_mcangle_it5.727.6428790
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A51678
12B51678
21A51378
22C51378
31A51120
32D51120
41B52728
42C52728
51B52378
52D52378
61C52166
62D52166
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 359 -
Rwork0.328 6327 -
all-6686 -
obs--99.26 %

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