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- PDB-8ozt: Crystal Structure of Fucosidase B -

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Basic information

Entry
Database: PDB / ID: 8ozt
TitleCrystal Structure of Fucosidase B
ComponentsAlpha-L-fucosidase
KeywordsSUGAR BINDING PROTEIN / 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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesLactobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsGallego del Sol, F. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
CitationJournal: To Be Published
Title: Crystal structure of fucosidase B
Authors: Gallego del Sol, F. / Marina, A.
History
DepositionMay 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list

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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
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase
E: Alpha-L-fucosidase
F: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,24332
Polymers281,1706
Non-polymers3,07326
Water15,133840
1
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,57422
Polymers187,4474
Non-polymers2,12718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15340 Å2
ΔGint-231 kcal/mol
Surface area60510 Å2
MethodPISA
2
E: Alpha-L-fucosidase
F: Alpha-L-fucosidase
hetero molecules

E: Alpha-L-fucosidase
F: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,33820
Polymers187,4474
Non-polymers1,89116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area14620 Å2
ΔGint-204 kcal/mol
Surface area60510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.457, 306.646, 169.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Alpha-L-fucosidase


Mass: 46861.742 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus (bacteria) / Gene: LC2W_2823 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A806E3N7
#2: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 3% PEG 8000, 26% MPD, 7% taximate pH5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.51→153.32 Å / Num. obs: 148303 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.09 / Rrim(I) all: 0.286 / Net I/σ(I): 7.9 / Num. measured all: 1512871
Reflection shellResolution: 2.51→2.64 Å / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 1.168 / Num. measured all: 224661 / Num. unique obs: 21532 / CC1/2: 0.716 / Rpim(I) all: 0.38 / Rrim(I) all: 1.23 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→153.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.556 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19979 7550 5.1 %RANDOM
Rwork0.16928 ---
obs0.17084 140419 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.326 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å20 Å2
2--0.9 Å2-0 Å2
3---0.49 Å2
Refinement stepCycle: 1 / Resolution: 2.51→153.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19501 0 208 840 20549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01220273
X-RAY DIFFRACTIONr_bond_other_d0.0010.01618605
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.65827691
X-RAY DIFFRACTIONr_angle_other_deg0.8051.57942659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72852424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.662594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.858103041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1870.23008
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0223575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024777
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4952.5439729
X-RAY DIFFRACTIONr_mcbond_other3.4952.5439729
X-RAY DIFFRACTIONr_mcangle_it5.4034.54612139
X-RAY DIFFRACTIONr_mcangle_other5.4034.54712140
X-RAY DIFFRACTIONr_scbond_it4.3512.95210544
X-RAY DIFFRACTIONr_scbond_other4.352.95310545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4715.24215552
X-RAY DIFFRACTIONr_long_range_B_refined7.89724.5822900
X-RAY DIFFRACTIONr_long_range_B_other7.90124.3922789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 527 -
Rwork0.265 10319 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1679-0.0719-0.07290.30950.17240.32670.03030.01730.02480.00620.027-0.0039-0.0383-0.0634-0.05730.03550.02530.0150.0772-0.0110.1902-48.4362-49.1525-2.2983
20.140.0192-0.00860.0646-0.04840.52140.00220.0215-0.00230.0228-0.0214-0.0182-0.06990.05570.01930.0189-0.01190.00490.1043-0.00470.1871-13.817-53.0512-15.0157
30.48050.3552-0.04540.2715-0.06720.428-0.0021-0.0017-0.04260.00770.0242-0.0316-0.0408-0.0428-0.02210.01850.01710.00710.09440.01660.172-41.4459-89.193919.945
40.8095-0.20330.28950.25320.01050.2485-0.0030.0666-0.1507-0.01860.06960.0242-0.02680.0508-0.06660.00890.00830.00260.1065-0.04990.1822-20.6-99.3944-9.4017
50.8243-0.4068-0.27870.36850.27550.2163-0.099-0.119-0.12490.02330.07980.0305-0.00270.06440.01920.07150.04180.01340.07360.03150.1716-62.4881-29.3106-31.0595
60.39740.11590.1210.35850.45290.6008-0.0242-0.02450.1114-0.06470.0332-0.0321-0.04570.0167-0.00910.1027-0.0343-0.02310.0222-0.03820.2083-60.57446.1501-42.388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 414
2X-RAY DIFFRACTION2B2 - 414
3X-RAY DIFFRACTION3C2 - 414
4X-RAY DIFFRACTION4D2 - 414
5X-RAY DIFFRACTION5E2 - 414
6X-RAY DIFFRACTION6F2 - 414

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