[English] 日本語
Yorodumi- PDB-7jfs: The structure of the CBM32-1, CBM32-2, and M60 catalytic domains ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jfs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of the CBM32-1, CBM32-2, and M60 catalytic domains from Clostridium perfringens ZmpB | |||||||||
Components | F5/8 type C domain proteinDiscoidin domain | |||||||||
Keywords | HYDROLASE / glycopeptidase | |||||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridium perfringens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.6 Å | |||||||||
Authors | Pluvinage, B. / Boraston, A.B. | |||||||||
Funding support | Canada, 2items
| |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Architecturally complex O -glycopeptidases are customized for mucin recognition and hydrolysis. Authors: Pluvinage, B. / Ficko-Blean, E. / Noach, I. / Stuart, C. / Thompson, N. / McClure, H. / Buenbrazo, N. / Wakarchuk, W. / Boraston, A.B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7jfs.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7jfs.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 7jfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/7jfs ftp://data.pdbj.org/pub/pdb/validation_reports/jf/7jfs | HTTPS FTP |
---|
-Related structure data
Related structure data | 7jnbC 7jndC 7jnfC 7jrlC 7jrmC 7js4C 5kdnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 112008.195 Da / Num. of mol.: 1 / Fragment: UNP residues 46-1003 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria) Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A Gene: CPF_1489 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2YN38, Hydrolases |
---|---|
#2: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.09 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2% Tascimate, 0.1 M Bis-Tris, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 4.6→30 Å / Num. obs: 9041 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.084 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 4.6→4.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 449 / CC1/2: 0.798 / Rpim(I) all: 0.387 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5KDN Resolution: 4.6→29.93 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.93 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 219.36 Å2 / Biso mean: 96.0881 Å2 / Biso min: 59.42 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.6→29.93 Å
| ||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
|