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Yorodumi- PDB-7js4: The structure of the M60 catalytic domain with the CBM51-1 and CB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7js4 | |||||||||
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Title | The structure of the M60 catalytic domain with the CBM51-1 and CBM51-2 domains from Clostridium perfringens ZmpB | |||||||||
Components | F5/8 type C domain protein | |||||||||
Keywords | HYDROLASE / glycopeptidase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium perfringens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.6 Å | |||||||||
Authors | Pluvinage, B. / Boraston, A.B. | |||||||||
Funding support | Canada, 2items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7js4.cif.gz | 202 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7js4.ent.gz | 156.5 KB | Display | PDB format |
PDBx/mmJSON format | 7js4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7js4_validation.pdf.gz | 404.4 KB | Display | wwPDB validaton report |
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Full document | 7js4_full_validation.pdf.gz | 407.3 KB | Display | |
Data in XML | 7js4_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 7js4_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/7js4 ftp://data.pdbj.org/pub/pdb/validation_reports/js/7js4 | HTTPS FTP |
-Related structure data
Related structure data | 7jfsC 7jnbC 7jndC 7jnfC 7jrlC 7jrmC 5kdnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 109575.055 Da / Num. of mol.: 1 / Fragment: UNP residues 497-1453 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 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.2 M potassium citrate tribasic monohydrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 13, 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: 6474 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.977 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.092 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 4.6→4.68 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 312 / CC1/2: 0.849 / Rpim(I) all: 0.348 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5KDN Resolution: 4.6→29.69 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.854 / SU B: 72.431 / SU ML: 0.873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 327.67 Å2 / Biso mean: 84.268 Å2 / Biso min: 26.25 Å2
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Refinement step | Cycle: final / Resolution: 4.6→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.6→4.718 Å / Rfactor Rfree error: 0
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