[English] 日本語
Yorodumi- PDB-1zuu: Crystal structure of the yeast Bzz1 first SH3 domain at 0.97-A re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zuu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the yeast Bzz1 first SH3 domain at 0.97-A resolution | ||||||
Components | BZZ1 protein | ||||||
Keywords | UNKNOWN FUNCTION / SH3 domain | ||||||
Function / homology | Function and homology information RND2 GTPase cycle / RHOQ GTPase cycle / actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / enzyme activator activity / response to salt stress / actin filament organization ...RND2 GTPase cycle / RHOQ GTPase cycle / actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / enzyme activator activity / response to salt stress / actin filament organization / phospholipid binding / endocytosis / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å | ||||||
Authors | Kursula, P. / Kursula, I. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M. | ||||||
Citation | Journal: To be Published Title: Structural genomics of yeast SH3 domains Authors: Kursula, P. / Kursula, I. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zuu.cif.gz | 45.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zuu.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 1zuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zuu_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1zuu_full_validation.pdf.gz | 427.2 KB | Display | |
Data in XML | 1zuu_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1zuu_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/1zuu ftp://data.pdbj.org/pub/pdb/validation_reports/zu/1zuu | HTTPS FTP |
-Related structure data
Related structure data | 1zukC 1zx6C 2a28C 1e6hS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 6382.083 Da / Num. of mol.: 1 / Fragment: first SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pDEST-17 / Production host: Escherichia coli (E. coli) / References: UniProt: P38822 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-UNX / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.5 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.976 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→20 Å / Num. all: 31881 / Num. obs: 31881 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 8.7 Å2 / Rsym value: 0.086 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 0.97→1 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2730 / Rsym value: 0.575 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1E6H Resolution: 0.97→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.55 / SU ML: 0.014 / Isotropic thermal model: anisotropic refinement / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.294 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 0.97→0.995 Å / Total num. of bins used: 20
|