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- PDB-7xsf: Crystal structure of ClAgl29A -

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Basic information

Entry
Database: PDB / ID: 7xsf
TitleCrystal structure of ClAgl29A
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / Glycoside hydrolase
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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Alpha-L-fucosidase
Similarity search - Component
Biological speciesCecembia lonarensis LW9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsShishiuchi, R. / Kang, H. / Tagami, T. / Okuyama, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K19159 Japan
CitationJournal: Acs Omega / Year: 2022
Title: Discovery of alpha-l-Glucosidase Raises the Possibility of alpha-l-Glucosides in Nature.
Authors: Shishiuchi, R. / Kang, H. / Tagami, T. / Ueda, Y. / Lang, W. / Kimura, A. / Okuyama, M.
History
DepositionMay 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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)132,5436
Polymers132,2982
Non-polymers2444
Water3,657203
1
A: Alpha-L-fucosidase
hetero molecules

B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,5436
Polymers132,2982
Non-polymers2444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area2790 Å2
ΔGint-12 kcal/mol
Surface area41520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.577, 95.521, 83.550
Angle α, β, γ (deg.)90.000, 97.331, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 24 - 573 / Label seq-ID: 23 - 572

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Alpha-L-fucosidase / alpha-L-glucosidase


Mass: 66149.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cecembia lonarensis LW9 (bacteria) / Gene: B879_03288 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: K1KZY4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsGenBank EKB28091.1

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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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M sodium citrate (pH 5.5), 16% PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→82.9 Å / Num. obs: 76908 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 42.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.09 / Rsym value: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 2.45 / Num. unique obs: 12196 / CC1/2: 0.9 / Rrim(I) all: 0.96 / Rsym value: 0.89 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XSD

2xsd


Resolution: 2.006→47.806 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.353 / SU ML: 0.195 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2427 3855 5.014 %
Rwork0.2046 73036 -
all0.207 --
obs-76891 98.848 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.108 Å2
Baniso -1Baniso -2Baniso -3
1--2.669 Å20 Å2-1.326 Å2
2--7.172 Å20 Å2
3----4.028 Å2
Refinement stepCycle: LAST / Resolution: 2.006→47.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8634 0 15 203 8852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0128915
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167855
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.64312074
X-RAY DIFFRACTIONr_angle_other_deg0.3811.56118387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97251050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.6461048
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.664101478
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.60510460
X-RAY DIFFRACTIONr_chiral_restr0.0550.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210138
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021878
X-RAY DIFFRACTIONr_nbd_refined0.1970.21683
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.27344
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24273
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.24346
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2332
X-RAY DIFFRACTIONr_metal_ion_refined0.1990.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.222
X-RAY DIFFRACTIONr_nbd_other0.1560.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.210
X-RAY DIFFRACTIONr_mcbond_it2.5684.4674212
X-RAY DIFFRACTIONr_mcbond_other2.5634.4674212
X-RAY DIFFRACTIONr_mcangle_it3.9446.6945258
X-RAY DIFFRACTIONr_mcangle_other3.9446.6955259
X-RAY DIFFRACTIONr_scbond_it2.6934.6824703
X-RAY DIFFRACTIONr_scbond_other2.6934.6824704
X-RAY DIFFRACTIONr_scangle_it4.2096.9136816
X-RAY DIFFRACTIONr_scangle_other4.2096.9136817
X-RAY DIFFRACTIONr_lrange_it5.76357.94810079
X-RAY DIFFRACTIONr_lrange_other5.76457.72210063
X-RAY DIFFRACTIONr_ncsr_local_group_10.0510.0518544
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.050670.0501
12AX-RAY DIFFRACTIONLocal ncs0.050670.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.006-2.0580.4232750.38551720.38757210.7620.77895.21060.339
2.058-2.1140.372750.35752540.35755880.7950.80598.94420.308
2.114-2.1760.3482690.33950870.3454070.8050.81799.05680.283
2.176-2.2420.3192620.32449570.32452740.8860.86598.95720.275
2.242-2.3160.3552490.30547420.30751260.8510.8997.36640.257
2.316-2.3970.2852460.27446660.27449470.9050.92899.29250.236
2.397-2.4870.292390.24545070.24747730.9320.9599.43430.212
2.487-2.5880.2482290.22143270.22345760.960.96399.56290.191
2.588-2.7030.2742190.21341560.21643970.950.9799.49970.189
2.703-2.8340.2582120.2139970.21342240.9580.97399.64490.19
2.834-2.9870.2492010.20338320.20640480.9590.97499.62940.188
2.987-3.1680.2321870.20235740.20437740.9660.97499.65550.191
3.168-3.3850.2381750.19633080.19835840.9630.97797.18190.19
3.385-3.6550.2381650.19531460.19733130.9630.97899.93960.193
3.655-4.0020.1821550.16329340.16430890.9810.9851000.166
4.002-4.470.1711380.14526240.14727660.9820.98899.85540.155
4.47-5.1540.1981230.1423380.14324630.9830.9999.91880.156
5.154-6.2940.2431060.15619720.1621100.9790.98898.48340.172
6.294-8.8250.204820.15515350.15716420.9780.98698.47750.174
8.825-47.8060.201480.1859080.1869580.9840.98199.79120.216

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