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Yorodumi- PDB-8k9z: Crystal structure of Vibrio vulnificus RID-dependent transforming... -
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-Basic information
Entry | Database: PDB / ID: 8k9z | |||||||||
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Title | Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin | |||||||||
Components |
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Keywords | TOXIN / MARTX toxin / RDTND-RID / NADase / CaM | |||||||||
Function / homology | Function and homology information Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / negative regulation of calcium ion transmembrane transporter activity / host cell cytosol / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / acyltransferase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / ligase activity ...Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / negative regulation of calcium ion transmembrane transporter activity / host cell cytosol / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / acyltransferase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / ligase activity / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cysteine-type peptidase activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / positive regulation of protein serine/threonine kinase activity / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / toxin activity / vesicle / transmembrane transporter binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / G protein-coupled receptor signaling pathway / centrosome / lipid binding / calcium ion binding / protein kinase binding / host cell plasma membrane / protein-containing complex / proteolysis / extracellular region / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Vibrio vulnificus (bacteria) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Lee, Y. / Choi, S. / Hwang, J. / Kim, M.H. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: To Be Published Title: Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin Authors: Lee, Y. / Choi, S. / Hwang, J. / Kim, M.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k9z.cif.gz | 225.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k9z.ent.gz | 178.4 KB | Display | PDB format |
PDBx/mmJSON format | 8k9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k9z_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8k9z_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8k9z_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 8k9z_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/8k9z ftp://data.pdbj.org/pub/pdb/validation_reports/k9/8k9z | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45959.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN52_02910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S3R7M0 #2: Protein | Mass: 16979.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal additional residues (GA) from expression vector after GST-tag removal by TEV protease. Source: (gene. exp.) Homo sapiens (human) / Gene: CALM2, CAM2, CAMB / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP24 #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.94 Å3/Da / Density % sol: 58.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 17% (w/v) PEG 3350 and 0.18 M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9797 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 31976 / % possible obs: 99.3 % / Redundancy: 6.3 % / CC1/2: 0.995 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.9→2.95 Å / Num. unique obs: 1543 / CC1/2: 0.581 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house model Resolution: 2.9→48.51 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.843 / Cross valid method: THROUGHOUT / ESU R Free: 0.537 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 48.475 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→48.51 Å
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