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- PDB-9jom: STRUCTURE OF ENDO-1,3-FUCANASE FUN168E FROM GH168 FAMILY -

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Basic information

Entry
Database: PDB / ID: 9jom
TitleSTRUCTURE OF ENDO-1,3-FUCANASE FUN168E 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 / Glycoside hydrolase superfamily / Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein
Function and homology information
Biological speciesWenyingzhuangia fucanilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 (Fun168E) at 2.04 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)45,5701
Polymers45,5701
Non-polymers00
Water7,044391
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)83.135, 83.135, 100.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

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Components

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


Mass: 45569.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria)
Gene: AXE80_08855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B1Y6K9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 10,000

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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: Jun 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.04→72 Å / Num. obs: 26154 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.084 / Rrim(I) all: 0.246 / Χ2: 1 / Net I/σ(I): 7.4 / Num. measured all: 199432
Reflection shellResolution: 2.04→2.15 Å / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.745 / Num. measured all: 17782 / Num. unique obs: 3769 / CC1/2: 0.73 / Rpim(I) all: 0.385 / Rrim(I) all: 0.842 / Χ2: 1.01 / Net I/σ(I) obs: 2.3

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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: 2.04→72 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 2014 7.71 %
Rwork0.1769 --
obs0.1813 26118 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 0 0 391 3278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022986
X-RAY DIFFRACTIONf_angle_d0.5364043
X-RAY DIFFRACTIONf_dihedral_angle_d5.462382
X-RAY DIFFRACTIONf_chiral_restr0.041410
X-RAY DIFFRACTIONf_plane_restr0.003518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.32021420.2391689X-RAY DIFFRACTION100
2.09-2.150.23461420.21971683X-RAY DIFFRACTION100
2.15-2.210.26151400.21261716X-RAY DIFFRACTION100
2.21-2.280.30121450.20521703X-RAY DIFFRACTION100
2.28-2.360.26521420.21021695X-RAY DIFFRACTION100
2.36-2.460.26391400.19931698X-RAY DIFFRACTION100
2.46-2.570.26711420.20851696X-RAY DIFFRACTION100
2.57-2.70.24861430.19011723X-RAY DIFFRACTION100
2.7-2.870.22951460.18741726X-RAY DIFFRACTION100
2.87-3.090.24061410.17691722X-RAY DIFFRACTION100
3.09-3.410.22211460.17121709X-RAY DIFFRACTION100
3.41-3.90.23961480.14491748X-RAY DIFFRACTION100
3.9-4.90.17291440.13111754X-RAY DIFFRACTION100
4.92-720.20721530.17421842X-RAY DIFFRACTION100

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