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- PDB-8ya7: endo-1,3-fucanase Fun168A,complex with fucotetraose -

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Basic information

Entry
Database: PDB / ID: 8ya7
Titleendo-1,3-fucanase Fun168A,complex with fucotetraose
Componentsendo-1,3-fucanase
KeywordsHYDROLASE / endo-1 / 3-fucanase / GH168
Function / homologyHypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Uncharacterized protein
Function and homology information
Biological speciesWenyingzhuangia fucanilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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: Strucutre of endo-1,3-fucanase Fun168A complex with fucotetrose at 1.99 Angstroms resolution.
Authors: Chen, G.N. / Chang, Y.G.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: endo-1,3-fucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2322
Polymers48,3101
Non-polymers9231
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.017, 67.290, 239.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-590-

HOH

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Components

#1: Protein endo-1,3-fucanase


Mass: 48309.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria)
Gene: AXE80_10060 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B1Y779
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose- ...alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose


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


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium iodide+0.1 M MES pH6.5+27% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.99→119.91 Å / Num. obs: 28229 / % possible obs: 91.8 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.071 / Rrim(I) all: 0.183 / Χ2: 0.99 / Net I/σ(I): 8.4 / Num. measured all: 183912
Reflection shellResolution: 1.99→2.09 Å / % possible obs: 76 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.815 / Num. measured all: 22041 / Num. unique obs: 3350 / CC1/2: 0.794 / Rpim(I) all: 0.339 / Rrim(I) all: 0.885 / Χ2: 0.91 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→39.97 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 2000 7.1 %
Rwork0.1953 --
obs0.1995 28159 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 57 487 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113048
X-RAY DIFFRACTIONf_angle_d1.3344123
X-RAY DIFFRACTIONf_dihedral_angle_d6.609397
X-RAY DIFFRACTIONf_chiral_restr0.065436
X-RAY DIFFRACTIONf_plane_restr0.011512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.29121520.21191991X-RAY DIFFRACTION100
2.04-2.090.2801780.21671025X-RAY DIFFRACTION51
2.09-2.150.27121550.20052020X-RAY DIFFRACTION100
2.15-2.220.25641510.20411975X-RAY DIFFRACTION100
2.22-2.30.29551210.20651580X-RAY DIFFRACTION78
2.3-2.390.26021560.19342047X-RAY DIFFRACTION100
2.39-2.50.27091520.19971993X-RAY DIFFRACTION100
2.5-2.640.2731540.19922005X-RAY DIFFRACTION100
2.64-2.80.29371200.20871578X-RAY DIFFRACTION77
2.8-3.020.24371560.20242041X-RAY DIFFRACTION100
3.02-3.320.2571570.19752051X-RAY DIFFRACTION100
3.32-3.80.23491320.18241725X-RAY DIFFRACTION85
3.8-4.790.22841500.16751967X-RAY DIFFRACTION94
4.79-100.24071660.20882161X-RAY DIFFRACTION99

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