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- PDB-9jof: COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) FROM GH168 FAMIL... -

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Basic information

Entry
Database: PDB / ID: 9jof
TitleCOMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) FROM GH168 FAMILY WITH FUCOTRIOSE
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: 1.5 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) from GH168 family with fucotriose at 1.50 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:
MolmilJmol/JSmol

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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)97,4044
Polymers96,0112
Non-polymers1,3932
Water25,5271417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint3 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.819, 138.329, 63.062
Angle α, β, γ (deg.)90.00, 113.79, 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 alpha-L-fucopyranose-(1-3)-2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 696.629 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a1221m-1a_1-5_2*OSO/3=O/3=O][a1221m-1a_1-5_2*OSO/3=O/3=O_4*OSO/3=O/3=O][a1221m-1a_1-5]/1-2-3/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][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.: 1417 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 10% v/v 2-Propanol+20% w/v Polyethylene glycol 4,000+1 M HEPES sodium,pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.5→50.16 Å / Num. obs: 135276 / % possible obs: 98.8 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Χ2: 0.97 / Net I/σ(I): 18.8 / Num. measured all: 430391
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 90.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.147 / Num. measured all: 13077 / Num. unique obs: 6100 / CC1/2: 0.958 / Rpim(I) all: 0.118 / Rrim(I) all: 0.19 / Χ2: 0.86 / Net I/σ(I) obs: 5.1

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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: 1.5→30.24 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1691 1996 1.48 %
Rwork0.141 --
obs0.1414 135219 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→30.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5850 0 86 1417 7353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086091
X-RAY DIFFRACTIONf_angle_d1.098288
X-RAY DIFFRACTIONf_dihedral_angle_d12.975840
X-RAY DIFFRACTIONf_chiral_restr0.06918
X-RAY DIFFRACTIONf_plane_restr0.0081048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.22351330.17868754X-RAY DIFFRACTION91
1.54-1.580.21131360.16029389X-RAY DIFFRACTION97
1.58-1.630.17931350.15359477X-RAY DIFFRACTION99
1.63-1.680.18831480.15269529X-RAY DIFFRACTION100
1.68-1.740.17561480.15149582X-RAY DIFFRACTION100
1.74-1.810.17671450.14999599X-RAY DIFFRACTION100
1.81-1.890.19461450.14569601X-RAY DIFFRACTION100
1.89-1.990.16871400.14419557X-RAY DIFFRACTION100
1.99-2.110.16761430.14139612X-RAY DIFFRACTION100
2.11-2.280.17081380.13439601X-RAY DIFFRACTION100
2.28-2.510.14561450.13259601X-RAY DIFFRACTION100
2.51-2.870.16151460.13519632X-RAY DIFFRACTION100
2.87-3.610.17151440.13599617X-RAY DIFFRACTION100
3.61-30.240.15741500.13859672X-RAY DIFFRACTION99

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