[English] 日本語
Yorodumi- PDB-8xmz: Crystal structure of a novel porphyran-binding carbohydrate bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xmz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a novel porphyran-binding carbohydrate binding module | ||||||
Components | T9SS C-terminal target domain-containing protein | ||||||
Keywords | SUGAR BINDING PROTEIN / A novel porphyran-binding carbohydrate binding module | ||||||
Function / homology | Function and homology information cellular anatomical entity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Aquimarina sp. BL5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Mei, X.W. / Chang, Y.G. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of a novel porphyran-binding carbohydrate binding module Authors: Mei, X.W. / Chang, Y.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8xmz.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8xmz.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 8xmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/8xmz ftp://data.pdbj.org/pub/pdb/validation_reports/xm/8xmz | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18319.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Carbohydrate binding module / Source: (gene. exp.) Aquimarina sp. BL5 (bacteria) / Gene: D1818_19300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A9W2N2 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.31 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v Polyethylene glycol monomethyl ether 5,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.81 Å / Num. obs: 21013 / % possible obs: 99.9 % / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.021 / Rrim(I) all: 0.094 / Χ2: 0.99 / Net I/σ(I): 26.3 / Num. measured all: 398629 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible obs: 99.8 % / Redundancy: 19.8 % / Rmerge(I) obs: 1.158 / Num. measured all: 45470 / Num. unique obs: 2302 / CC1/2: 0.979 / Rpim(I) all: 0.264 / Rrim(I) all: 1.188 / Χ2: 0.96 / Net I/σ(I) obs: 3.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.95 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.89 / 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: 2.5→32.95 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|