+Open data
-Basic information
Entry | Database: PDB / ID: 3q7p | ||||||
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Title | Crystal Structure of Rad G-domain-GTP Analog Complex | ||||||
Components | GTP-binding protein RAD | ||||||
Keywords | SIGNALING PROTEIN / G-domain / G-protein / Cav2 beta | ||||||
Function / homology | Function and homology information NGF-stimulated transcription / small GTPase-mediated signal transduction / calcium channel regulator activity / calmodulin binding / GTPase activity / GTP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sasson, Y. / Navon-Perry, L. / Hirsch, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: RGK Family G-Domain:GTP Analog Complex Structures and Nucleotide-Binding Properties. Authors: Sasson, Y. / Navon-Perry, L. / Huppert, D. / Hirsch, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q7p.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q7p.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 3q7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q7p_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3q7p_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3q7p_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3q7p_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/3q7p ftp://data.pdbj.org/pub/pdb/validation_reports/q7/3q7p | HTTPS FTP |
-Related structure data
Related structure data | 3q72C 3q7qC 3q85C 2dpxS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18231.715 Da / Num. of mol.: 2 / Fragment: G-domain, residues 90-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RRAD, RAD / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / References: UniProt: P55042 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.15 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 25% PEG 400, 5% ethylene glycol 0.1M MES, 0.2M calcium acetate,, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 8487 / Num. obs: 8487 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB:2DPX Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / SU B: 13.832 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 41.401 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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