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- PDB-9int: Crystal structure of the complex of the beta,kappa-carrageenase C... -

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Basic information

Entry
Database: PDB / ID: 9int
TitleCrystal structure of the complex of the beta,kappa-carrageenase Cgbk16A from Wenyingzhuangia fucanilytica with an oligosaccharide of furcellaran
ComponentsGH16 domain-containing protein
KeywordsHYDROLASE / complex / Carrageenase / GH16_13 / Glucoside hydrolase / oligotetrasaccharide / furcellaran
Function / homology: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / GH16 domain-containing protein
Function and homology information
Biological speciesWenyingzhuangia fucanilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsChang, Y. / Chen, F.
Funding support1items
OrganizationGrant numberCountry
Other government2023YFD2100605
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Structural Insights into the Substrate Recognition and Catalytic Mechanism of a GH16 beta kappa-Carrageenase from Wenyingzhuangia fucanilytica.
Authors: Chen, F. / Xue, C. / Chen, G. / Mei, X. / Zheng, L. / Chang, Y.
History
DepositionJul 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH16 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3772
Polymers37,2801
Non-polymers1,0971
Water7,873437
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.770, 76.930, 99.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GH16 domain-containing protein / carrageenase


Mass: 37279.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria)
Gene: AXE80_10150 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B1Y771
#2: Polysaccharide 3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha- ...3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 1096.941 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,6,5/[a2112h-1b_1-5][a2112h-1a_1-5_3-6][a2112h-1b_1-5_4*OSO/3=O/3=O]/1-2-3-2-3-2/a3-b1_b4-c1_c3-d1_d4-e1_e3-f1WURCSPDB2Glycan 1.1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 25.5% PEG 4000, 15% Glycerol, 0.17 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.56→40.58 Å / Num. obs: 52972 / % possible obs: 97.86 % / Redundancy: 12.7 % / Biso Wilson estimate: 20.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 27.9
Reflection shellResolution: 1.56→1.62 Å / Mean I/σ(I) obs: 5.5 / Num. unique obs: 51770 / CC1/2: 0.963 / % possible all: 93.74

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→40.58 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 17.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 1403 2.71 %
Rwork0.1582 --
obs0.1588 51771 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→40.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 72 437 2852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.023
X-RAY DIFFRACTIONf_dihedral_angle_d8.085308
X-RAY DIFFRACTIONf_chiral_restr0.066359
X-RAY DIFFRACTIONf_plane_restr0.007430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.620.21451310.17414749X-RAY DIFFRACTION94
1.62-1.680.22611390.17884821X-RAY DIFFRACTION95
1.68-1.760.20161370.17534883X-RAY DIFFRACTION97
1.76-1.850.17331350.16194958X-RAY DIFFRACTION97
1.85-1.970.19691400.16085034X-RAY DIFFRACTION98
1.97-2.120.17281410.16155052X-RAY DIFFRACTION99
2.12-2.330.17721430.15775106X-RAY DIFFRACTION99
2.33-2.670.22681440.16435168X-RAY DIFFRACTION100
2.67-3.360.17211460.1595187X-RAY DIFFRACTION100
3.36-40.580.14541470.14645410X-RAY DIFFRACTION100

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