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- PDB-7db5: Crystal structure of alpha-L-fucosidase from Vibrio sp. strain EJY3 -

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Basic information

Entry
Database: PDB / ID: 7db5
TitleCrystal structure of alpha-L-fucosidase from Vibrio sp. strain EJY3
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / PHOSPHATE ION
Function and homology information
Biological speciesVibrio sp. EJY3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHong, H. / Kim, K.-J.
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Dual alpha-1,4- and beta-1,4-Glycosidase Activities by the Novel Carbohydrate-Binding Module in alpha-l-Fucosidase from Vibrio sp. Strain EJY3.
Authors: Hong, H. / Kim, D.H. / Seo, H. / Kim, K.H. / Kim, K.J.
History
DepositionOct 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1845
Polymers71,8131
Non-polymers3714
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-4 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.916, 163.916, 58.712
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Alpha-L-fucosidase


Mass: 71812.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio sp. EJY3 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Sodium dihydrogen phosphate, Potassium hydrogen phosphate, acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 67820 / % possible obs: 95.3 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.081 / Χ2: 2.513 / Net I/σ(I): 12.8 / Num. measured all: 515865
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.937.60.32834330.9520.1260.3521.92796.8
1.93-1.977.50.28633890.9630.110.3072.03596.7
1.97-2.017.60.2434360.9710.0920.2582.10496.7
2.01-2.057.60.21434170.9750.0830.232.16496.8
2.05-2.097.60.19334000.9790.0740.2072.25995.9
2.09-2.147.60.16833840.9830.0650.182.33796.8
2.14-2.197.60.15334300.9850.0590.1652.40496.7
2.19-2.257.70.13433980.9890.0510.1442.44595.7
2.25-2.327.70.12734180.990.0480.1362.46696.5
2.32-2.397.70.11733840.9910.0440.1252.49896.1
2.39-2.487.70.10434250.9920.040.1122.48796.2
2.48-2.587.70.133980.9930.0380.1072.595.7
2.58-2.77.70.08934040.9940.0330.0952.52395.7
2.7-2.847.80.0833970.9940.030.0862.53595.4
2.84-3.027.80.07333870.9960.0270.0792.64595.1
3.02-3.257.80.06733860.9960.0250.0712.81694.7
3.25-3.587.70.05833710.9960.0220.0622.98494.6
3.58-4.097.50.05533570.9960.0210.0592.98393.4
4.09-5.167.10.05332860.9960.0210.0573.01391.4
5.16-507.20.05833200.9950.0230.0633.25689.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.204 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 3393 5 %RANDOM
Rwork0.1707 ---
obs0.1723 64319 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.4 Å2 / Biso mean: 23.593 Å2 / Biso min: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.9→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 23 305 5121
Biso mean--34.3 27.32 -
Num. residues----586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134969
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174319
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.6446759
X-RAY DIFFRACTIONr_angle_other_deg1.4741.57510066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1795593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79823.344299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32115778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5231527
X-RAY DIFFRACTIONr_chiral_restr0.090.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025628
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021065
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 240 -
Rwork0.199 4751 -
all-4991 -
obs--95.39 %

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