+Open data
-Basic information
Entry | Database: PDB / ID: 3hpc | ||||||
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Title | Crystal structure of SNX5-PX domain in P21 space group | ||||||
Components | Snx5 protein | ||||||
Keywords | PROTEIN TRANSPORT / Sprting nexin / SNX5 / Phox / SNX5-PX / PhosphatidylInositol / PI(4 / 5)P2 / CELL ADHESION | ||||||
Function / homology | Function and homology information epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / Golgi Associated Vesicle Biogenesis / phosphatidylinositol-5-phosphate binding / retromer complex / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding ...epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / Golgi Associated Vesicle Biogenesis / phosphatidylinositol-5-phosphate binding / retromer complex / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / dynactin binding / phagocytic cup / brush border / D1 dopamine receptor binding / positive regulation of insulin receptor signaling pathway / ruffle / negative regulation of blood pressure / phosphatidylinositol binding / intracellular protein transport / cytoplasmic side of plasma membrane / endosome / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Koharudin, L.M.I. / Furey, W. / Gronenborn, A.M. | ||||||
Citation | Journal: To be Published Title: The Phox domain of sorting nexin 5 lacks ptdins(3)p specificity and preferentially binds to ptdins(4,5)P2 Authors: Koharudin, L.M.I. / Furey, W. / Liu, H. / Liu, Y.-J. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hpc.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hpc.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 3hpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpc ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpc | HTTPS FTP |
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-Related structure data
Related structure data | 3hpbSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18508.824 Da / Num. of mol.: 1 / Fragment: Residues 20-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Snx5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1H267 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Sequence details | THE ORIGINAL CONSTRUCT CONTAINED RESIDUES 1-180. THE FINAL CRYSTALLIZED PROTEIN CONSTRUCT SPANS ...THE ORIGINAL CONSTRUCT CONTAINED RESIDUES 1-180. THE FINAL CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.300956 Å3/Da / Density % sol: 46.543972 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: The protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml and crystallization were obtained using an optimized ...Details: The protein solution in the final superdex-75 buffer (20 mM Tris.HCl, 100 mM NaCl, 0.02% NaN3, pH 8.0) was concentrated to 8 mg/ml and crystallization were obtained using an optimized crystallization condition of 8ul of protein vs 1ul of reservoir solution (0.2M NH4CH3COO, 0.1M Sodium cacodylate tryhydrate pH 6.5, 30% PEG 4000), VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 15, 2007 / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→31.12 Å / Num. obs: 28322 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 4.13 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.47→1.52 Å / Redundancy: 2.65 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 1.4 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HPB Resolution: 1.47→31.12 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.265 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.085 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→31.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.51 Å / Total num. of bins used: 20
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