+Open data
-Basic information
Entry | Database: PDB / ID: 1i49 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF ARFAPTIN | ||||||
Components | ARFAPTIN 2 | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to phagophore assembly site / GTP-dependent protein binding / ruffle organization / phosphatidylinositol-4-phosphate binding / lamellipodium assembly / small GTPase-mediated signal transduction / mitophagy ...membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to phagophore assembly site / GTP-dependent protein binding / ruffle organization / phosphatidylinositol-4-phosphate binding / lamellipodium assembly / small GTPase-mediated signal transduction / mitophagy / ruffle / trans-Golgi network membrane / phospholipid binding / intracellular protein transport / small GTPase binding / cell cortex / actin cytoskeleton organization / cadherin binding / protein domain specific binding / GTP binding / nucleolus / Golgi apparatus / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Tarricone, C. / Xiao, B. / Justin, N. / Gamblin, S.J. / Smerdon, S.J. | ||||||
Citation | Journal: Nature / Year: 2001 Title: The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways. Authors: Tarricone, C. / Xiao, B. / Justin, N. / Walker, P.A. / Rittinger, K. / Gamblin, S.J. / Smerdon, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i49.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i49.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/1i49 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/1i49 | 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: 25614.057 Da / Num. of mol.: 2 / Fragment: RESIDUES 118-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P53365 #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: 4.99 Å3/Da / Density % sol: 75.35 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: TRI-SODIUM CITRATE DIHYDRATE, ISOPROPANOL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→30 Å / Num. all: 25459 / Num. obs: 25169 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 28.9 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.8→2.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.309 / Num. unique all: 3134 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 |