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Open data
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Basic information
Entry | Database: PDB / ID: 1va7 | ||||||
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Title | Yeast Myo3 SH3 domain, triclinic crystal form | ||||||
![]() | Myosin-3 isoform | ||||||
![]() | CONTRACTILE PROTEIN / Structural genomics / SH3 domain | ||||||
Function / homology | ![]() bipolar cellular bud site selection / myosin I complex / actin cortical patch localization / positive regulation of Arp2/3 complex-mediated actin nucleation / fungal-type cell wall organization / cell tip / actin cortical patch / reticulophagy / response to osmotic stress / microfilament motor activity ...bipolar cellular bud site selection / myosin I complex / actin cortical patch localization / positive regulation of Arp2/3 complex-mediated actin nucleation / fungal-type cell wall organization / cell tip / actin cortical patch / reticulophagy / response to osmotic stress / microfilament motor activity / myosin binding / exocytosis / actin filament organization / cell periphery / endocytosis / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kursula, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M. | ||||||
![]() | ![]() Title: High-throughput structural genomics of yeast SH3 domains Authors: Kursula, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.6 KB | Display | ![]() |
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PDB format | ![]() | 43.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ruwS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 3 - 61 / Label seq-ID: 3 - 61
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Details | each chain is an independent biological unit |
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Components
#1: Protein | Mass: 7645.547 Da / Num. of mol.: 4 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pDEST17 / Production host: ![]() ![]() #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: sodium citrate, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8115 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 6221 / Num. obs: 6221 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.106 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 609 / Rsym value: 0.406 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RUW Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.846 / SU B: 24.02 / SU ML: 0.436 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS parameters used / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.484 / Stereochemistry target values: Engh & Huber / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.195 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 860 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.9→2.974 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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