+Open data
-Basic information
Entry | Database: PDB / ID: 1ynz | ||||||
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Title | SH3 domain of yeast Pin3 | ||||||
Components | Pin3p | ||||||
Keywords | PROTEIN BINDING / SH3 domain | ||||||
Function / homology | Function and homology information Recycling pathway of L1 / RHOV GTPase cycle / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / Antigen processing: Ubiquitination & Proteasome degradation / Neutrophil degranulation / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kursula, P. / Kursula, I. / Zou, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M. | ||||||
Citation | Journal: To be Published Title: Structural analysis of the yeast SH3 domain proteome Authors: Kursula, P. / Kursula, I. / Zou, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ynz.cif.gz | 22.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ynz.ent.gz | 13.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ynz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1ynz ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1ynz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6516.325 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: GenBank: 6325412, UniProt: Q06449*PLUS |
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#2: 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: 2.1 Å3/Da / Density % sol: 42 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 2805 / Num. obs: 2805 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.109 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 347 / Rsym value: 0.307 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.87 / SU B: 6.762 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.389 / ESU R Free: 0.233 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.405 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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