+Open data
-Basic information
Entry | Database: PDB / ID: 5jd0 | ||||||
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Title | crystal structure of ARAP3 RhoGAP domain | ||||||
Components | Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 | ||||||
Keywords | SIGNALING PROTEIN / ARAP3 / RhoGAP | ||||||
Function / homology | Function and homology information phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / ruffle / cytoskeleton organization / RAC1 GTPase cycle / lamellipodium ...phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / ruffle / cytoskeleton organization / RAC1 GTPase cycle / lamellipodium / cytoskeleton / signal transduction / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Bao, H. / Li, F. / Wu, J. / Shi, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Basis for the Specific Recognition of RhoA by the Dual GTPase-activating Protein ARAP3 Authors: Bao, H. / Li, F. / Wang, C. / Wang, N. / Jiang, Y. / Tang, Y. / Wu, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jd0.cif.gz | 171.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jd0.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jd0_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 5jd0_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 5jd0_validation.xml.gz | 16 KB | Display | |
Data in CIF | 5jd0_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/5jd0 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jd0 | HTTPS FTP |
-Related structure data
Related structure data | 5jcpC 2ee5S C: citing same article (ref.) 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: 24185.779 Da / Num. of mol.: 2 / Fragment: UNP residues 906-1107 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARAP3 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8WWN8 #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: 3.04 Å3/Da / Density % sol: 59.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 100 mM HEPES, 10% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→76.728 Å / Num. all: 25608 / Num. obs: 25608 / % possible obs: 99.1 % / Redundancy: 9.1 % / Biso Wilson estimate: 36.17 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.147 / Rsym value: 0.138 / Net I/av σ(I): 3.304 / Net I/σ(I): 11.1 / Num. measured all: 232624 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EE5 Resolution: 2.3→38.364 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→38.364 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.8014 Å / Origin y: -39.1162 Å / Origin z: 11.9869 Å
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Refinement TLS group | Selection details: all |