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- PDB-9jos: STRUCTURE OF ENDO-1,3-FUCANASE FROM GH168 FAMILY -

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Basic information

Entry
Database: PDB / ID: 9jos
TitleSTRUCTURE OF ENDO-1,3-FUCANASE FROM GH168 FAMILY
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 / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
Function and homology information
Biological speciesNovipirellula artificiosorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Structure of endo-1.3-fucanase from GH168 family at 1.70 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,7671
Polymers46,7671
Non-polymers00
Water7,927440
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)148.280, 148.280, 42.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 46766.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novipirellula artificiosorum (bacteria)
Gene: Poly41_55130 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5C6D8T6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 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: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.7→74.14 Å / Num. obs: 37521 / % possible obs: 99 % / Redundancy: 9.1 % / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.027 / Rrim(I) all: 0.084 / Χ2: 0.95 / Net I/σ(I): 20.4 / Num. measured all: 343059
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.075 / Num. unique obs: 2549 / CC1/2: 0.624 / Rpim(I) all: 0.505 / Rrim(I) all: 1.193 / Χ2: 0.86

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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: 1.7→74.14 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 1994 5.32 %
Rwork0.1661 --
obs0.1682 37516 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→74.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 0 440 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012985
X-RAY DIFFRACTIONf_angle_d1.0694039
X-RAY DIFFRACTIONf_dihedral_angle_d6.28391
X-RAY DIFFRACTIONf_chiral_restr0.056408
X-RAY DIFFRACTIONf_plane_restr0.01522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.34391320.29612343X-RAY DIFFRACTION91
1.74-1.790.33471400.27482445X-RAY DIFFRACTION97
1.79-1.840.2471430.22982516X-RAY DIFFRACTION98
1.84-1.90.26261450.19592560X-RAY DIFFRACTION100
1.9-1.970.2681460.19992576X-RAY DIFFRACTION100
1.97-2.050.21831430.18862550X-RAY DIFFRACTION100
2.05-2.140.22821410.17482576X-RAY DIFFRACTION100
2.14-2.250.23211430.15752563X-RAY DIFFRACTION100
2.25-2.40.21961430.17042560X-RAY DIFFRACTION100
2.4-2.580.1651400.15752566X-RAY DIFFRACTION100
2.58-2.840.20871460.17472577X-RAY DIFFRACTION100
2.84-3.250.22111430.15752571X-RAY DIFFRACTION100
3.25-4.090.16331460.14632562X-RAY DIFFRACTION100
4.1-74.140.17561430.14082557X-RAY DIFFRACTION100

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