[English] 日本語
Yorodumi- PDB-7jnd: The structure of CBM32-1 and CBM32-2 domains from Clostridium per... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jnd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of CBM32-1 and CBM32-2 domains from Clostridium perfringens ZmpB | |||||||||
Components | F5/8 type C domain protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / Carbohydrate binding module | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium perfringens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 | 7jnd.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7jnd.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 7jnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jnd_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7jnd_full_validation.pdf.gz | 438.1 KB | Display | |
Data in XML | 7jnd_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 7jnd_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/7jnd ftp://data.pdbj.org/pub/pdb/validation_reports/jn/7jnd | HTTPS FTP |
-Related structure data
Related structure data | 7jfsC 7jnbSC 7jnfC 7jrlC 7jrmC 7js4C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 51421.480 Da / Num. of mol.: 1 / Fragment: Carbohydrate binding module (UNP residues 28-453) 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 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.17 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.18 M calcium chloride, 20% PEG3350, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91966 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 11, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91966 Å / Relative weight: 1 |
Reflection | Resolution: 2→51.53 Å / Num. obs: 31552 / % possible obs: 96.5 % / Redundancy: 6.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.069 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4198 / CC1/2: 0.756 / Rpim(I) all: 0.285 / % possible all: 89.9 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7JNB Resolution: 2→41.16 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.039 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.65 Å2 / Biso mean: 30.224 Å2 / Biso min: 13.9 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→41.16 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|