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- PDB-9jp3: COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE MUTANT D171A WITH FUCOTETRAOSE -

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Basic information

Entry
Database: PDB / ID: 9jp3
TitleCOMPLEX STRUCTURE OF ENDO-1,3-FUCANASE MUTANT D171A WITH FUCOTETRAOSE
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: 1.4 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 mutant D171A with fucotetraose at 1.40 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6462
Polymers46,7231
Non-polymers9231
Water9,692538
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)152.782, 152.782, 42.337
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-853-

HOH

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Components

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


Mass: 46722.719 Da / Num. of mol.: 1 / Mutation: D171A
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: 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.: 1 / 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.: 538 / 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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) PEG 3000, 100 mM CHES/ Sodium hydroxide pH 9.5

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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 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.4→44.1 Å / Num. obs: 72761 / % possible obs: 99.7 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.024 / Rrim(I) all: 0.074 / Χ2: 0.91 / Net I/σ(I): 17.8 / Num. measured all: 693360
Reflection shellResolution: 1.4→1.47 Å / % possible obs: 97.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.657 / Num. measured all: 75097 / Num. unique obs: 10449 / CC1/2: 0.793 / Rpim(I) all: 0.258 / Rrim(I) all: 0.708 / Χ2: 0.71 / Net I/σ(I) obs: 2.8

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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→44.1 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1741 1976 2.72 %
Rwork0.1572 --
obs0.1577 72736 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 57 538 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083050
X-RAY DIFFRACTIONf_angle_d1.1224142
X-RAY DIFFRACTIONf_dihedral_angle_d6.908395
X-RAY DIFFRACTIONf_chiral_restr0.075431
X-RAY DIFFRACTIONf_plane_restr0.009522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.26541360.2394885X-RAY DIFFRACTION96
1.43-1.470.2421420.2195053X-RAY DIFFRACTION99
1.47-1.510.21681430.20015093X-RAY DIFFRACTION100
1.51-1.560.20241390.18675042X-RAY DIFFRACTION100
1.56-1.620.21951390.19275072X-RAY DIFFRACTION100
1.62-1.680.19691450.17615105X-RAY DIFFRACTION100
1.68-1.760.19831390.17615034X-RAY DIFFRACTION100
1.76-1.850.19781450.16415056X-RAY DIFFRACTION100
1.85-1.970.17751430.16475070X-RAY DIFFRACTION100
1.97-2.120.17011410.15155082X-RAY DIFFRACTION100
2.12-2.340.1611420.15415052X-RAY DIFFRACTION100
2.34-2.670.1711380.14625078X-RAY DIFFRACTION100
2.67-3.370.17691440.15185060X-RAY DIFFRACTION100
3.37-44.10.1391400.13395078X-RAY DIFFRACTION100

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