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- PDB-4j27: Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroi... -

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Basic information

Entry
Database: PDB / ID: 4j27
TitleCrystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in a novel crystal form
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / Alpha-L-fucosidase
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
IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsWright, D.W.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Three dimensional structure of a bacterial alpha-l-fucosidase with a 5-membered iminocyclitol inhibitor.
Authors: Wright, D.W. / Moreno-Vargas, A.J. / Carmona, A.T. / Robina, I. / Davies, G.J.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,26015
Polymers104,1622
Non-polymers1,09813
Water19,0781059
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5957
Polymers52,0811
Non-polymers5146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6648
Polymers52,0811
Non-polymers5847
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.150, 96.550, 97.270
Angle α, β, γ (deg.)90.000, 91.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 35 - 471 / Label seq-ID: 1 - 437

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alpha-L-fucosidase


Mass: 52080.930 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8A3I4
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1059 / 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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17% PEG 6K, 0.124M ammonium sulfate, 0.1M imidazole 2 parts protein: 3 mother liquor, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.59→30.666 Å / Num. all: 164706 / Num. obs: 164706 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.112 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.59-1.683.70.8780.988387239670.87899.9
1.68-1.783.80.5831.385810227210.583100
1.78-1.93.80.3692.180897213360.369100
1.9-2.053.80.2213.475563198670.221100
2.05-2.253.80.1475.169763183020.147100
2.25-2.523.80.17.463417165760.1100
2.52-2.93.80.0749.556011146080.074100
2.9-3.563.80.0669.247642124090.066100
3.56-5.033.80.053113679695930.053100
5.03-30.6663.80.03417.42003853270.03499.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVV

2wvv


Resolution: 1.59→30.666 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1694 / WRfactor Rwork: 0.1497 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8693 / SU B: 1.577 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0654 / SU Rfree: 0.0655 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 8454 5 %RANDOM
Rwork0.1577 ---
obs0.1587 159881 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.97 Å2 / Biso mean: 15.8145 Å2 / Biso min: 5.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å2-0.29 Å2
2--0.03 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.59→30.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7075 0 69 1059 8203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.027468
X-RAY DIFFRACTIONr_bond_other_d0.0050.026815
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.93710159
X-RAY DIFFRACTIONr_angle_other_deg1.056315719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03624.157356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.888151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7641536
X-RAY DIFFRACTIONr_chiral_restr0.0970.21035
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218480
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021798
X-RAY DIFFRACTIONr_mcbond_it1.1011.3123549
X-RAY DIFFRACTIONr_mcbond_other1.11.3113548
X-RAY DIFFRACTIONr_mcangle_it1.7191.9624444
Refine LS restraints NCS

Ens-ID: 1 / Number: 26913 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.591→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 662 -
Rwork0.288 11719 -
all-12381 -
obs--99.93 %

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