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Yorodumi- PDB-8br1: ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MART... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8br1 | ||||||
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Title | ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to Latrunculin-B-ATP-Mg-actin, and 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE and 2 Mg ions | ||||||
Components |
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Keywords | TOXIN / bacterial nucleotidyl cyclase toxin / activated complex | ||||||
Function / homology | Function and homology information calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / host cell cytosol / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle ...calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / host cell cytosol / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / toxin activity / cell body / transferase activity / hydrolase activity / protein domain specific binding / cysteine-type endopeptidase activity / calcium ion binding / positive regulation of gene expression / host cell plasma membrane / magnesium ion binding / proteolysis / extracellular region / ATP binding / identical protein binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio nigripulchritudo (bacteria) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.044 Å | ||||||
Authors | Teixeira-Nunes, M. / Renault, L. / Retailleau, P. | ||||||
Funding support | France, 1items
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Citation | Journal: Plos Pathog. / Year: 2023 Title: Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin. Authors: Teixeira-Nunes, M. / Retailleau, P. / Raoux-Barbot, D. / Comisso, M. / Missinou, A.A. / Velours, C. / Plancqueel, S. / Ladant, D. / Mechold, U. / Renault, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8br1.cif.gz | 618.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8br1.ent.gz | 508.3 KB | Display | PDB format |
PDBx/mmJSON format | 8br1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8br1_validation.pdf.gz | 4.7 MB | Display | wwPDB validaton report |
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Full document | 8br1_full_validation.pdf.gz | 4.7 MB | Display | |
Data in XML | 8br1_validation.xml.gz | 60.3 KB | Display | |
Data in CIF | 8br1_validation.cif.gz | 85.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/8br1 ftp://data.pdbj.org/pub/pdb/validation_reports/br/8br1 | HTTPS FTP |
-Related structure data
Related structure data | 8bjhC 8bjiC 8bjjC 8bo1C 8br0C 2pavS 7pj0 7psb 7q9d S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 41862.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P68135 #2: Protein | Mass: 46247.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio nigripulchritudo (bacteria) / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N3LUE9, adenylate cyclase |
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-Non-polymers , 8 types, 664 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / | #9: Chemical | ChemComp-PEO / | #10: Water | ChemComp-HOH / | |
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-Details
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: 2.58 Å3/Da / Density % sol: 52.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 26 % peg 3350, 26 % Glycerol, 30 mM LiSO4, 0.1M TrisHCl pH8.5, 3 % Dioxane, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.044→47.76 Å / Num. obs: 86495 / % possible obs: 84.3 % / Redundancy: 32.7 % / Biso Wilson estimate: 54.49 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.044→2.21 Å / Rmerge(I) obs: 3.852 / Num. unique obs: 4319 / % possible all: 28.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PAV Resolution: 2.044→47.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.253 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.19
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Displacement parameters | Biso max: 124.86 Å2 / Biso mean: 61.71 Å2 / Biso min: 35.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.044→47.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.044→2.15 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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