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- PDB-8zbv: alpha-L-fucosidase from Pontiella sulfatireligans F21 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8zbv
Titlealpha-L-fucosidase from Pontiella sulfatireligans F21
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / GH family 95 / Pontiella sulfatireligans F21 kiritimatiellaeota
Function / homology
Function and homology information


alpha-L-fucosidase activity / carbohydrate metabolic process
Similarity search - Function
Alpha-L-fucosidase / : / : / Glycoside hydrolase family 95, C-terminal domain / Glycosyl hydrolase family 95 catalytic domain / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / Six-hairpin glycosidase superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosyl hydrolase, all-beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesPontiella sulfatireligans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhao, P. / Bai, L. / Wang, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Study on the function and diversity of key enzymes degrading fucoidan in Kiritimatiellaeota
Authors: Zhao, P. / Bai, L. / Wang, S.
History
DepositionApr 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-L-fucosidase


Theoretical massNumber of molelcules
Total (without water)96,6261
Polymers96,6261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.293, 106.204, 72.598
Angle α, β, γ (deg.)90.000, 91.840, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Alpha-L-fucosidase


Mass: 96626.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pontiella sulfatireligans (bacteria) / Gene: SCARR_01153 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6C2UI12
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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 6000, Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.3→33.55 Å / Num. obs: 12058 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 55.23 Å2 / CC1/2: 0.984 / Net I/σ(I): 6.8
Reflection shellResolution: 3.3→3.56 Å / Num. unique obs: 12058 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→33.55 Å / SU ML: 0.4073 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2638 604 5.02 %
Rwork0.228 11419 -
obs0.2298 12023 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.29 Å2
Refinement stepCycle: LAST / Resolution: 3.3→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 0 0 6175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256345
X-RAY DIFFRACTIONf_angle_d0.55398604
X-RAY DIFFRACTIONf_chiral_restr0.042888
X-RAY DIFFRACTIONf_plane_restr0.00471122
X-RAY DIFFRACTIONf_dihedral_angle_d4.7293836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.630.31941370.29022833X-RAY DIFFRACTION99.56
3.63-4.160.28931940.24842803X-RAY DIFFRACTION99.6
4.16-5.230.24571460.21012854X-RAY DIFFRACTION99.54
5.23-33.550.21891270.19722929X-RAY DIFFRACTION99.64
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)
11.659518482790.06699061584330.970100846661.004461891250.05702172912831.84685653425-0.01008472866280.218800687288-0.0443348469126-0.110242850063-0.0255991883021-0.0243655247478-0.145640862753-0.100638172040.03935698709460.301952662102-0.007778726549880.02613211827930.4018799043090.014632111140.34408824734613.5134816717-1.056307342025.64116917672
22.05861170845-0.9001949260480.5634758624980.71390018867-0.2473186693791.492251847830.171739939340.405374723263-0.0863486544438-0.33736282428-0.0124758244577-0.07677581804320.09881641601380.0386513491578-0.2055827483230.413111262679-0.07472120177730.03276107799230.440252786472-0.07437038052650.38431834824120.6808928053-3.90735207668-4.3930925325
32.27114597753-0.03381483709630.5822963554321.906013703330.02686843213280.651921546842-0.279767685104-0.3396047987510.3373932890780.1418033162820.128222141901-0.158937220212-0.2868924932620.0572126228790.1392127035080.4454593138150.0786280907974-0.1041948904430.377027738447-0.04968250769810.39758106517630.44669694076.6348029825121.7416871042
41.819241155520.02185057654760.8731119987771.306190877770.08032073873282.094043999940.0574393042626-0.0775155057895-0.3490058709980.0776634914155-0.0158906491339-0.3018631430970.1613700138930.023789429897-0.04288628427910.3457697044740.0473098140106-0.04758470576560.337444263544-0.02534432361330.49161063390439.0702990352-9.2774252379324.0260245152
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 62 through 280 )62 - 2801 - 219
22chain 'A' and (resid 281 through 383 )281 - 383220 - 319
33chain 'A' and (resid 384 through 599 )384 - 599320 - 535
44chain 'A' and (resid 600 through 840 )600 - 840536 - 765

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