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Yorodumi- PDB-3kn1: Crystal Structure of Golgi Phosphoprotein 3 N-term Truncation Variant -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kn1 | ||||||
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Title | Crystal Structure of Golgi Phosphoprotein 3 N-term Truncation Variant | ||||||
Components | Golgi phosphoprotein 3 | ||||||
Keywords | PROTEIN BINDING / beta hairpin / phosphoinositide binding domain / Cell membrane / Cytoplasm / Endosome / Golgi apparatus / Membrane / Mitochondrion / Phosphoprotein | ||||||
Function / homology | Function and homology information asymmetric Golgi ribbon formation / cellular response to rapamycin / Golgi vesicle budding / glycoprotein biosynthetic process / Golgi cisterna / protein retention in Golgi apparatus / Golgi ribbon formation / Golgi to plasma membrane protein transport / leukocyte tethering or rolling / cell adhesion molecule production ...asymmetric Golgi ribbon formation / cellular response to rapamycin / Golgi vesicle budding / glycoprotein biosynthetic process / Golgi cisterna / protein retention in Golgi apparatus / Golgi ribbon formation / Golgi to plasma membrane protein transport / leukocyte tethering or rolling / cell adhesion molecule production / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phosphatidylinositol-4-phosphate binding / regulation of mitochondrion organization / lamellipodium assembly / Golgi cisterna membrane / Golgi organization / protein secretion / positive regulation of TOR signaling / positive regulation of protein secretion / trans-Golgi network / mitochondrial intermembrane space / cell migration / gene expression / endosome / intracellular membrane-bounded organelle / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / mitochondrion / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | ||||||
Authors | Schmitz, K.R. / Bessman, N.J. / Setty, T.G. / Ferguson, K.M. | ||||||
Citation | Journal: J.Cell Biol. / Year: 2009 Title: PtdIns4P recognition by Vps74/GOLPH3 links PtdIns 4-kinase signaling to retrograde Golgi trafficking. Authors: Wood, C.S. / Schmitz, K.R. / Bessman, N.J. / Setty, T.G. / Ferguson, K.M. / Burd, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kn1.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kn1.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 3kn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/3kn1 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/3kn1 | HTTPS FTP |
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-Related structure data
Related structure data | 2zihS 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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Details | authors state that the software-determined 24-mer involves interactions stabilized by non-physiological inter-copy disulfide bonds between symmetry-related copies of chain A. |
-Components
#1: Protein | Mass: 28792.574 Da / Num. of mol.: 1 / Fragment: UNP residues 52-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOLPH3, GPP34 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q9H4A6 | ||
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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: 3.84 Å3/Da / Density % sol: 67.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.9 M (NH4)2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97951 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 10180 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.133 / Χ2: 1.67 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.4 / Num. unique all: 994 / Χ2: 1.393 / % possible all: 99.6 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZIH Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.816 / SU R Cruickshank DPI: 0.637 / SU Rfree: 0.354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.637 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 109.27 Å2 / Biso mean: 38.227 Å2 / Biso min: 11.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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