+Open data
-Basic information
Entry | Database: PDB / ID: 8jiy | ||||||
---|---|---|---|---|---|---|---|
Title | A carbohydrate binding domain of a putative chondroitinase | ||||||
Components | DUF4955 domain-containing protein | ||||||
Keywords | SUGAR BINDING PROTEIN / Carbohydrate binding | ||||||
Function / homology | Domain of unknown function DUF4955 / Domain of unknown function (DUF4955) / Secretion system C-terminal sorting domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Secretion system C-terminal sorting domain / Pectin lyase fold / Pectin lyase fold/virulence factor / DUF4955 domain-containing protein Function and homology information | ||||||
Biological species | Polaribacter haliotis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Liu, G.C. / Chang, Y.G. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Identification and structural characterization of a novel chondroitin sulfate-specific carbohydrate-binding module: The first member of a new family, CBM100. Authors: Liu, G. / Chang, Y. / Mei, X. / Chen, G. / Zhang, Y. / Jiang, X. / Tao, W. / Xue, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jiy.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jiy.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 8jiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jiy_validation.pdf.gz | 420.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jiy_full_validation.pdf.gz | 420.9 KB | Display | |
Data in XML | 8jiy_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 8jiy_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/8jiy ftp://data.pdbj.org/pub/pdb/validation_reports/ji/8jiy | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27117.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Polaribacter haliotis (bacteria) / Gene: H9I45_07735 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7L8AJZ3 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.77 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→43.89 Å / Num. obs: 32725 / % possible obs: 99.4 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.026 / Rrim(I) all: 0.062 / Χ2: 0.97 / Net I/σ(I): 17 / Num. measured all: 169904 |
Reflection shell | Resolution: 1.55→1.58 Å / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.238 / Num. measured all: 6887 / Num. unique obs: 1596 / CC1/2: 0.937 / Rpim(I) all: 0.127 / Rrim(I) all: 0.271 / Χ2: 0.56 / Net I/σ(I) obs: 4.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→29.56 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.62 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→29.56 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|