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Yorodumi- PDB-8x3a: Solution NMR structure of cellulosomal double-dockerin module of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8x3a | ||||||
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Title | Solution NMR structure of cellulosomal double-dockerin module of Clo1313_0689 from Clostridium thermocellum | ||||||
Components | Serine protease | ||||||
Keywords | PROTEIN BINDING / CALCIUM-BINDING PROTEIN | ||||||
Function / homology | Function and homology information polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / serine-type endopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Acetivibrio thermocellus DSM 1313 (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Chen, C. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Protein Sci. / Year: 2024 Title: A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features. Authors: Chen, C. / Yang, H. / Dong, S. / You, C. / Morais, S. / Bayer, E.A. / Liu, Y.J. / Xuan, J. / Cui, Q. / Mizrahi, I. / Feng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x3a.cif.gz | 893.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x3a.ent.gz | 746.4 KB | Display | PDB format |
PDBx/mmJSON format | 8x3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/8x3a ftp://data.pdbj.org/pub/pdb/validation_reports/x3/8x3a | HTTPS FTP |
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-Related structure data
Related structure data | 8x39C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16627.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria) Gene: cprA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2HPT9 | ||
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#2: Chemical | ChemComp-CA / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.6 mM [U-13C; U-15N] dDoc_0689, 50 mM sodium acetate, 50 mM potassium chloride, 10 mM CaCl2, 3 mg/L DTT, 0.02 % w/v DSS, 90% H2O/10% D2O Label: sample1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 mM / Label: condition1 / pH: 4.9 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 3 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |