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Yorodumi- PDB-2bx6: Crystal Structure of the human Retinitis Pigmentosa protein 2 (RP2) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bx6 | ||||||
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Title | Crystal Structure of the human Retinitis Pigmentosa protein 2 (RP2) | ||||||
Components | XRP2 PROTEIN | ||||||
Keywords | TRANSDUCTION PROTEIN / RETINITIS PIGMENTOSA / SENSORY TRANSDUCTION / VISION | ||||||
Function / homology | Function and homology information Trafficking of myristoylated proteins to the cilium / periciliary membrane compartment / post-Golgi vesicle-mediated transport / cilium assembly / visual perception / centriole / GTPase activator activity / ciliary basal body / cilium / unfolded protein binding ...Trafficking of myristoylated proteins to the cilium / periciliary membrane compartment / post-Golgi vesicle-mediated transport / cilium assembly / visual perception / centriole / GTPase activator activity / ciliary basal body / cilium / unfolded protein binding / protein transport / protein folding / cytoplasmic vesicle / nuclear body / GTP binding / Golgi apparatus / magnesium ion binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Kuhnel, K. / Veltel, S. / Schlichting, I. / Wittinghofer, A. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Crystal Structure of the Human Retinitis Pigmentosa 2 Protein and its Interaction with Arl3 Authors: Kuhnel, K. / Veltel, S. / Schlichting, I. / Wittinghofer, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bx6.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bx6.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/2bx6 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/2bx6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39682.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O75695 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | pH: 7.5 / Details: 1.8 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97923 |
Detector | Date: Dec 20, 2003 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 24188 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.9 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.485 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.19 / ESU R Free: 0.169 / 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: 32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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