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Yorodumi- PDB-2gnc: Crystal structure of srGAP1 SH3 domain in the slit-robo signaling... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gnc | ||||||
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Title | Crystal structure of srGAP1 SH3 domain in the slit-robo signaling pathway | ||||||
Components | SLIT-ROBO Rho GTPase-activating protein 1 | ||||||
Keywords | SIGNALING PROTEIN / BETA BARREL | ||||||
Function / homology | Function and homology information : / small GTPase binding => GO:0031267 / small GTPase binding => GO:0031267 / Rho protein signal transduction / GTPase activator activity / negative regulation of cell migration / cell migration / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Li, X. / Liu, Y. / Gao, F. / Bartlam, M. / Wu, J.Y. / Rao, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural Basis of Robo Proline-rich Motif Recognition by the srGAP1 Src Homology 3 Domain in the Slit-Robo Signaling Pathway Authors: Li, X. / Chen, Y. / Liu, Y. / Gao, J. / Gao, F. / Bartlam, M. / Wu, J.Y. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gnc.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gnc.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 2gnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gnc_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
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Full document | 2gnc_full_validation.pdf.gz | 429 KB | Display | |
Data in XML | 2gnc_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2gnc_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/2gnc ftp://data.pdbj.org/pub/pdb/validation_reports/gn/2gnc | HTTPS FTP |
-Related structure data
Related structure data | 1bk2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6752.610 Da / Num. of mol.: 2 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q91Z69 #2: 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: 2.14 Å3/Da / Density % sol: 42.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5M Lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 11938 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.81→1.87 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK2 Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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