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- PDB-9jog: COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) WITH FUCOTETRAOS... -

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Basic information

Entry
Database: PDB / ID: 9jog
TitleCOMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) WITH FUCOTETRAOSE FROM HOLOTHURIA TUBULOSA
Componentsendo-1.3-fucanase
KeywordsHYDROLASE / Endo-1.3-fucanase / GH168
Function / homologyHypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Uncharacterized protein
Function and homology information
Biological speciesWenyingzhuangia fucanilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 (Fun168D) with fucotetraose from Holothuria tubulosa at 1.40 Angstroms resulution.
Authors: Chen, G.N. / Chang, Y.G.
History
DepositionSep 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: endo-1.3-fucanase
B: endo-1.3-fucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8564
Polymers96,0112
Non-polymers1,8462
Water25,3111405
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)54.741, 138.390, 62.866
Angle α, β, γ (deg.)90.00, 113.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein endo-1.3-fucanase


Mass: 48005.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria)
Gene: AXE80_08865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B1Y6G8
#2: Polysaccharide 2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose- ...2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-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.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
[][a-L-Fucp2SO3]{[(3+1)][a-L-Fucp2SO3]{[(3+1)][a-L-Fucp]{[(3+1)][a-L-Fucp2SO34SO3]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1405 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium acetate trihydrate, 0.1M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.4→39.83 Å / Num. obs: 167694 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.055 / Χ2: 1.01 / Net I/σ(I): 21.2 / Num. measured all: 1095501
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.277 / Num. measured all: 53878 / Num. unique obs: 8239 / CC1/2: 0.967 / Rpim(I) all: 0.116 / Rrim(I) all: 0.301 / Χ2: 1.03 / Net I/σ(I) obs: 6.7

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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: 1.4→34.6 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1553 2006 1.2 %
Rwork0.1402 --
obs0.1404 167589 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5903 0 114 1405 7422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086231
X-RAY DIFFRACTIONf_angle_d1.288496
X-RAY DIFFRACTIONf_dihedral_angle_d7.081826
X-RAY DIFFRACTIONf_chiral_restr0.098947
X-RAY DIFFRACTIONf_plane_restr0.0081073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.17231390.170511805X-RAY DIFFRACTION100
1.44-1.470.16861490.163511770X-RAY DIFFRACTION100
1.47-1.520.18751400.159611797X-RAY DIFFRACTION100
1.52-1.570.15541450.15111844X-RAY DIFFRACTION100
1.57-1.620.16231470.14711798X-RAY DIFFRACTION100
1.62-1.690.1861410.147111765X-RAY DIFFRACTION100
1.69-1.760.14341440.14411862X-RAY DIFFRACTION100
1.76-1.860.15771390.143411830X-RAY DIFFRACTION100
1.86-1.970.17341470.144511798X-RAY DIFFRACTION100
1.97-2.130.14631420.133311829X-RAY DIFFRACTION100
2.13-2.340.16681400.131211821X-RAY DIFFRACTION100
2.34-2.680.15751400.133511854X-RAY DIFFRACTION100
2.68-3.370.1361440.138611868X-RAY DIFFRACTION100
3.37-34.60.1481490.135111942X-RAY DIFFRACTION100

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