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- PDB-9ijc: Crystal structure of the beta,kappa-carrageenase Cgbk16A from Wen... -

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Basic information

Entry
Database: PDB / ID: 9ijc
TitleCrystal structure of the beta,kappa-carrageenase Cgbk16A from Wenyingzhuangia fucanilytica
ComponentsGH16 domain-containing protein
KeywordsHYDROLASE / Apo / Carrageenase / GH16_13 / Glucoside hydrolase
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: 1.52 Å
AuthorsChang, Y. / Chen, F.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2023YFD2100605 China
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
DepositionJun 22, 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


Theoretical massNumber of molelcules
Total (without water)37,2801
Polymers37,2801
Non-polymers00
Water6,684371
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)46.370, 76.833, 100.329
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting 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: Apr 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.52→50.16 Å / Num. obs: 55782 / % possible obs: 97.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05349 / Rpim(I) all: 0.01554 / Rrim(I) all: 0.05577 / Net I/σ(I): 21.5
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.2553 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5175 / CC1/2: 0.986 / Rpim(I) all: 0.07313 / Rrim(I) all: 0.2658 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→50.16 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1824 3.33 %
Rwork0.1702 --
obs0.1708 54735 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→50.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 0 371 2709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.975
X-RAY DIFFRACTIONf_dihedral_angle_d7.122304
X-RAY DIFFRACTIONf_chiral_restr0.066328
X-RAY DIFFRACTIONf_plane_restr0.007428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.22381340.21393855X-RAY DIFFRACTION94
1.56-1.610.22481330.19823908X-RAY DIFFRACTION95
1.61-1.660.20721370.18133929X-RAY DIFFRACTION96
1.66-1.720.25221380.17343971X-RAY DIFFRACTION97
1.72-1.790.18041400.16844042X-RAY DIFFRACTION98
1.79-1.870.17741400.17614022X-RAY DIFFRACTION98
1.87-1.970.21271380.18054035X-RAY DIFFRACTION98
1.97-2.090.1691420.16174091X-RAY DIFFRACTION98
2.09-2.250.16171410.16254107X-RAY DIFFRACTION100
2.25-2.480.18961430.17124159X-RAY DIFFRACTION99
2.48-2.840.19141430.17974148X-RAY DIFFRACTION99
2.84-3.570.18041450.15794241X-RAY DIFFRACTION100
3.57-100.18771500.16774403X-RAY DIFFRACTION100

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