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

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Basic information

Entry
Database: PDB / ID: 9joh
TitleCOMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) WITH FUCOTETRAOSE FROM ISOSTICHOPUS BADIONOTUS
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: 1.36 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 Isostichopus badionotus at 1.36 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)97,8564
Polymers96,0112
Non-polymers1,8462
Water26,2301456
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)54.659, 138.577, 63.038
Angle α, β, γ (deg.)90.00, 113.77, 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-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.: 2 / 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.: 1456 / 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: 45.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 24% PEG1500 +20% Glycerol

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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: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.36→69.29 Å / Num. obs: 182984 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.021 / Rrim(I) all: 0.038 / Χ2: 0.82 / Net I/σ(I): 17.6 / Num. measured all: 597467
Reflection shellResolution: 1.36→1.43 Å / % possible obs: 99.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.293 / Num. measured all: 71933 / Num. unique obs: 26739 / CC1/2: 0.892 / Rpim(I) all: 0.209 / Rrim(I) all: 0.361 / Χ2: 0.61 / Net I/σ(I) obs: 2.6

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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: 1.36→30.22 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1632 1982 1.08 %
Rwork0.1457 --
obs0.1459 182917 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 0 114 1456 7467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126162
X-RAY DIFFRACTIONf_angle_d1.3618392
X-RAY DIFFRACTIONf_dihedral_angle_d7.276812
X-RAY DIFFRACTIONf_chiral_restr0.095938
X-RAY DIFFRACTIONf_plane_restr0.0091057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.2471380.218612904X-RAY DIFFRACTION100
1.39-1.430.22311400.20212942X-RAY DIFFRACTION100
1.43-1.470.21351400.191112895X-RAY DIFFRACTION100
1.47-1.520.18211490.182312897X-RAY DIFFRACTION100
1.52-1.570.19991380.166112913X-RAY DIFFRACTION100
1.57-1.640.15621410.158912914X-RAY DIFFRACTION100
1.64-1.710.1841460.153712957X-RAY DIFFRACTION100
1.71-1.80.16151370.150312916X-RAY DIFFRACTION100
1.8-1.920.17741410.149412892X-RAY DIFFRACTION100
1.92-2.060.17391430.139112888X-RAY DIFFRACTION99
2.06-2.270.1571410.132512952X-RAY DIFFRACTION100
2.27-2.60.14151430.132912949X-RAY DIFFRACTION100
2.6-3.270.15631410.139312896X-RAY DIFFRACTION99
3.27-30.220.14731440.136113020X-RAY DIFFRACTION99

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