+Open data
-Basic information
Entry | Database: PDB / ID: 4h0y | ||||||
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Title | Crystal structure of NAD+-Ia(E380S)-actin complex | ||||||
Components |
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Keywords | TOXIN/STRUCTURAL PROTEIN / ADP-ribosyltransferase / TOXIN-STRUCTURAL PROTEIN complex | ||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / 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 / cell body / hydrolase activity / protein domain specific binding / nucleotide binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular region / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Clostridium perfringens (bacteria) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Tsurumura, T. / Oda, M. / Nagahama, M. / Tsuge, H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex Authors: Tsurumura, T. / Tsumori, Y. / Qiu, H. / Oda, M. / Sakurai, J. / Nagahama, M. / Tsuge, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h0y.cif.gz | 324.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h0y.ent.gz | 259.7 KB | Display | PDB format |
PDBx/mmJSON format | 4h0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/4h0y ftp://data.pdbj.org/pub/pdb/validation_reports/h0/4h0y | HTTPS FTP |
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-Related structure data
Related structure data | 4gy2C 4h03SC 4h0tC 4h0vC 4h0xC C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 48177.145 Da / Num. of mol.: 1 / Mutation: E380S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q46220, NAD+-protein-arginine ADP-ribosyltransferase |
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#2: Protein | Mass: 41862.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P68135 |
-Non-polymers , 7 types, 318 molecules
#3: Chemical | ChemComp-NAD / | ||||||||
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#4: Chemical | ChemComp-PO4 / | ||||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CA / | #7: Chemical | ChemComp-ATP / | #8: Chemical | ChemComp-LAR / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.51 % |
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Crystal grow | Temperature: 277.13 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG1500, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.13K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. all: 83936 / Num. obs: 83852 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 4.9 / Num. unique all: 4121 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4H03 Resolution: 1.94→30.91 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.514 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.135 / 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: 33.207 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→30.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.941→1.991 Å / Total num. of bins used: 20
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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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