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- PDB-4j28: Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroi... -

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Basic information

Entry
Database: PDB / ID: 4j28
TitleCrystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in complex with a 5-membered iminocyclitol inhibitor
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Alpha-L-fucosidase / HYDROLASE-HYDROLASE INHIBITOR complex
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-EAT / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides Thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,61116
Polymers104,1622
Non-polymers1,44914
Water13,133729
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,04011
Polymers52,0811
Non-polymers95910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5715
Polymers52,0811
Non-polymers4914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.728, 95.611, 96.988
Angle α, β, γ (deg.)90.000, 91.210, 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 - 472 / Label seq-ID: 1 - 438

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

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 743 molecules

#2: Chemical ChemComp-EAT / (2S,3S,4R,5S)-2-(1H-benzimidazol-2-yl)-5-methylpyrrolidine-3,4-diol


Mass: 233.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N3O2
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10.45% PEG 6K, 0.12M ammonium sulfate, 0.095M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.73→29.013 Å / Num. all: 128218 / Num. obs: 128218 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.045 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.73-1.823.20.4491.756453179140.44994.5
1.82-1.933.20.3442.258100179170.34499.6
1.93-2.073.40.2123.356638168920.21299.8
2.07-2.233.30.1425.151448156540.14299.6
2.23-2.453.30.09846972144230.0999.5
2.45-2.743.30.05712.743459130130.05799.2
2.74-3.163.10.04116.135624113990.04198.6
3.16-3.873.20.028223038394860.02896.9
3.87-5.473.10.02425.22269273820.02496.9
5.47-29.0133.20.01734.91341441380.01797.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J27

4j27


Resolution: 1.73→29.01 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1821 / WRfactor Rwork: 0.1593 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7446 / SU B: 3.238 / SU ML: 0.092 / SU R Cruickshank DPI: 0.0895 / SU Rfree: 0.0873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4J28 TO BUILD A STARTING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4J28 TO BUILD A STARTING MODEL DIRECTLY. THE RFREE FLAG FROM 4J27 WAS USED FOR THIS DATASET.
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 6409 5 %RANDOM
Rwork0.1706 ---
obs0.1717 128119 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.9 Å2 / Biso mean: 34.2843 Å2 / Biso min: 20.87 Å2
Baniso -1Baniso -2Baniso -3
1-4.24 Å20 Å2-0.86 Å2
2---0.23 Å20 Å2
3----3.98 Å2
Refinement stepCycle: LAST / Resolution: 1.73→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 96 729 7852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027403
X-RAY DIFFRACTIONr_bond_other_d0.0050.026679
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9410075
X-RAY DIFFRACTIONr_angle_other_deg1.0473.00215378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44824.097349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.653151177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.551535
X-RAY DIFFRACTIONr_chiral_restr0.1030.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218401
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021796
X-RAY DIFFRACTIONr_mcbond_it2.4343.2083526
X-RAY DIFFRACTIONr_mcbond_other2.4333.2073525
X-RAY DIFFRACTIONr_mcangle_it3.1564.84410
Refine LS restraints NCS

Ens-ID: 1 / Number: 26587 / 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: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 408 -
Rwork0.332 8106 -
all-8514 -
obs--89.26 %

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