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- PDB-9joo: COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168E) WITH FUCOTETRAOSES -

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Basic information

Entry
Database: PDB / ID: 9joo
TitleCOMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168E) WITH FUCOTETRAOSES
ComponentsGlycoside-hydrolase family GH114 TIM-barrel domain-containing protein
KeywordsHYDROLASE / Endo-1.3-fucanase / GH168
Function / homologyHypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Glycoside hydrolase superfamily / Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
Function and homology information
Biological speciesWenyingzhuangia fucanilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsChen, G.N. / Chang, Y.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U22A20542 China
CitationJournal: To Be Published
Title: Complex structure of endo-1.3-fucanase (Fun168E) with fucotetraoses at 1.97 Angstroms resulution.
Authors: Chen, G.N. / Chang, Y.G.
History
DepositionSep 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4153
Polymers45,5701
Non-polymers1,8462
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.450, 79.560, 81.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein


Mass: 45569.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria)
Gene: AXE80_08855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B1Y6K9
#2: Polysaccharide 2-O-sulfo-alpha-L-fucopyranose-(1-3)-alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose- ...2-O-sulfo-alpha-L-fucopyranose-(1-3)-alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 922.833 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
[][a-L-Fucp2SO3]{[(3+1)][a-L-Fucp2SO34SO3]{[(3+1)][a-L-Fucp]{[(3+1)][a-L-Fucp2SO3]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.97→48.62 Å / Num. obs: 28598 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.045 / Rrim(I) all: 0.163 / Χ2: 0.99 / Net I/σ(I): 12.6 / Num. measured all: 362205
Reflection shellResolution: 1.97→2.02 Å / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 1.477 / Num. measured all: 27776 / Num. unique obs: 2098 / CC1/2: 0.773 / Rpim(I) all: 0.417 / Rrim(I) all: 1.535 / Χ2: 0.94 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→48.62 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 2012 7.05 %
Rwork0.1818 --
obs0.1845 28547 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 114 340 3389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073139
X-RAY DIFFRACTIONf_angle_d1.044273
X-RAY DIFFRACTIONf_dihedral_angle_d8.39392
X-RAY DIFFRACTIONf_chiral_restr0.059453
X-RAY DIFFRACTIONf_plane_restr0.007523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.30781410.25771877X-RAY DIFFRACTION100
2.02-2.070.27191410.24681877X-RAY DIFFRACTION100
2.07-2.130.2821370.23611847X-RAY DIFFRACTION100
2.13-2.20.28841410.21351866X-RAY DIFFRACTION100
2.2-2.280.26761490.21421869X-RAY DIFFRACTION100
2.28-2.370.27121390.20051882X-RAY DIFFRACTION100
2.37-2.480.23861420.19181902X-RAY DIFFRACTION100
2.48-2.610.2541410.19641854X-RAY DIFFRACTION100
2.61-2.780.25251410.20751894X-RAY DIFFRACTION100
2.78-2.990.23751420.18851889X-RAY DIFFRACTION100
2.99-3.290.21991450.18291896X-RAY DIFFRACTION100
3.29-3.770.19051510.16021914X-RAY DIFFRACTION100
3.77-4.750.17871480.14161937X-RAY DIFFRACTION100
4.75-48.620.18451540.16882031X-RAY DIFFRACTION99

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