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- PDB-7xsg: Crystal structure of ClAgl29B -

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Basic information

Entry
Database: PDB / ID: 7xsg
TitleCrystal structure of ClAgl29B
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Alpha-L-fucosidase
Similarity search - Component
Biological speciesCecembia lonarensis LW9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.609 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 1.1Apr 3, 2024Group: 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)135,0179
Polymers134,3962
Non-polymers6217
Water18,1591008
1
A: Alpha-L-fucosidase
hetero molecules

B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0179
Polymers134,3962
Non-polymers6217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area2520 Å2
ΔGint-23 kcal/mol
Surface area43580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.132, 123.405, 166.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 33 - 586 / Label seq-ID: 34 - 587

Dom-ID
1
2

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

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 67198.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cecembia lonarensis LW9 (bacteria) / Gene: B879_03287 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: K1KV82

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Non-polymers , 5 types, 1015 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1008 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Sequence detailsGenBank EKB28090.1

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M sodium citrate (pH 3.5), 5% PEG 20,000, 5% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.609→99.165 Å / Num. obs: 194275 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.069 / Rsym value: 0.063 / Net I/σ(I): 22.17
Reflection shellResolution: 1.61→1.71 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.51 / Num. unique obs: 30357 / CC1/2: 0.942 / Rrim(I) all: 0.459 / Rsym value: 0.423 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 1.609→45.418 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.3 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1884 9719 5.003 %
Rwork0.1722 184555 -
all0.173 --
obs-194274 99.483 %
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: 18.001 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å2-0 Å20 Å2
2---0.245 Å2-0 Å2
3----0.795 Å2
Refinement stepCycle: LAST / Resolution: 1.609→45.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8828 0 40 1008 9876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129285
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168261
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.63412593
X-RAY DIFFRACTIONr_angle_other_deg0.4721.56219354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64951123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.7841036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.835101585
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.33410452
X-RAY DIFFRACTIONr_chiral_restr0.070.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021897
X-RAY DIFFRACTIONr_nbd_refined0.2230.21786
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.27621
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24430
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.24488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2684
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.227
X-RAY DIFFRACTIONr_nbd_other0.2070.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.243
X-RAY DIFFRACTIONr_mcbond_it1.6651.8334453
X-RAY DIFFRACTIONr_mcbond_other1.6631.8334453
X-RAY DIFFRACTIONr_mcangle_it2.4962.7365589
X-RAY DIFFRACTIONr_mcangle_other2.4962.7375590
X-RAY DIFFRACTIONr_scbond_it2.2752.0344832
X-RAY DIFFRACTIONr_scbond_other2.2752.0344833
X-RAY DIFFRACTIONr_scangle_it3.4882.9497004
X-RAY DIFFRACTIONr_scangle_other3.4882.9497005
X-RAY DIFFRACTIONr_lrange_it4.96127.66710860
X-RAY DIFFRACTIONr_lrange_other4.73424.09810569
X-RAY DIFFRACTIONr_ncsr_local_group_10.0860.0518979
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.086110.05009
12AX-RAY DIFFRACTIONLocal ncs0.086110.05009
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
1.609-1.6510.2616740.237127320.238143290.960.96993.55850.197
1.651-1.6960.2186960.211131960.212138980.9710.97499.95680.173
1.696-1.7450.2276780.2129130.201135950.970.97699.97060.163
1.745-1.7990.2076570.19124800.191131370.9730.9781000.156
1.799-1.8580.2146380.182121260.184127640.9730.9791000.151
1.858-1.9230.1976200.176117880.177124090.9780.9899.99190.147
1.923-1.9950.1885980.175113450.176119430.9780.9811000.15
1.995-2.0760.1915750.174109330.175115100.9750.98199.98260.153
2.076-2.1690.1795530.171104940.172110500.9810.98399.97280.152
2.169-2.2740.1915280.169100360.17105750.9780.98399.8960.153
2.274-2.3970.1865030.16395610.164100690.9780.98499.95030.147
2.397-2.5420.1594770.15790580.15795380.9840.98599.96850.146
2.542-2.7170.174500.15985670.1690170.9830.9851000.148
2.717-2.9330.1814210.1679700.16183940.9790.98499.96430.153
2.933-3.2120.1783860.16773510.16777380.980.98399.98710.165
3.212-3.5890.1973520.1766910.17170450.9760.98399.97160.173
3.589-4.140.1623120.15359240.15462380.9850.98599.96790.163
4.14-5.060.1662670.15550580.15553280.9860.98899.94370.173
5.06-7.1120.2152100.19639960.19742070.9790.98599.97620.213
7.112-45.4180.2221240.19723360.19824860.9760.97798.95410.222

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