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Yorodumi- PDB-2v1r: Yeast Pex13 SH3 domain complexed with a peptide from Pex14 at 2.1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v1r | ||||||
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Title | Yeast Pex13 SH3 domain complexed with a peptide from Pex14 at 2.1 A resolution | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / TRANSLOCATION / TRANSMEMBRANE / PEPTIDE COMPLEX / STRUCTURAL GENOMICS / PEROXISOME | ||||||
Function / homology | Function and homology information Class I peroxisomal membrane protein import / peroxisomal importomer complex / protein import into peroxisome matrix, docking / Peroxisomal protein import / E3 ubiquitin ligases ubiquitinate target proteins / peroxisomal membrane / protein transmembrane transporter activity / protein-macromolecule adaptor activity / signaling receptor binding Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kursula, I. / Kursula, P. / 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. / Pinotsis, N. / Lehmann, F. / Zou, P. / 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 | 2v1r.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v1r.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v1r_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 2v1r_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 2v1r_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2v1r_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1r ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1r | HTTPS FTP |
-Related structure data
Related structure data | 2v1qC 2vknC 1n5zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
#1: Protein | Mass: 9316.717 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 299-374 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): BL21(DE3) / References: UniProt: P80667 #2: Protein/peptide | Mass: 1721.952 Da / Num. of mol.: 3 / Fragment: SH3 DOMAIN BINDING SEGMENT, RESIDUES 83-96 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P53112 #3: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46.14 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→20 Å / Num. obs: 9925 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.11→2.25 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.6 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N5Z Resolution: 2.1→20 Å
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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