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Yorodumi- PDB-2wwe: Crystal structure of the phox homology domain of human phosphoino... -
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-Basic information
Entry | Database: PDB / ID: 2wwe | ||||||
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Title | Crystal structure of the phox homology domain of human phosphoinositide-3-kinase-C2-gamma | ||||||
Components | PHOSPHOINOSITIDE-3-KINASE, CLASS 2, GAMMA POLYPEPTIDE | ||||||
Keywords | TRANSFERASE / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / KINASE / PIK3C2G / MEMBRANE / PX-DOMAIN / ATP-BINDING / POLYMORPHISM / CLASS 2 PI3K | ||||||
Function / homology | Function and homology information : / : / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4-phosphate 3-kinase / phosphatidylinositol kinase activity / phosphatidylinositol biosynthetic process / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity ...: / : / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4-phosphate 3-kinase / phosphatidylinositol kinase activity / phosphatidylinositol biosynthetic process / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol binding / chemotaxis / cell migration / viral RNA genome replication / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotyenova, T. / Kotzch, A. / Kraulis, P. / Markova, N. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Van Der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Phox Homology Domain of Human Phosphoinositide-3-Kinase-C2-Gamma Authors: Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / ...Authors: Roos, A.K. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotyenova, T. / Kotzch, A. / Kraulis, P. / Markova, N. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wwe.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwe.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wwe_validation.pdf.gz | 415.7 KB | Display | wwPDB validaton report |
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Full document | 2wwe_full_validation.pdf.gz | 416.4 KB | Display | |
Data in XML | 2wwe_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 2wwe_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwe ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwe | HTTPS FTP |
-Related 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: 14977.646 Da / Num. of mol.: 1 / Fragment: PHOX HOMOLOGY DOMAIN, RESIDUES 1203-1306 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE / References: UniProt: A1L3U0, UniProt: O75747*PLUS |
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#2: 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: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.1M TRI-SODIUM CITRATE DIHYDRATE PH 5.5, 20% PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9789 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 24, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→29.16 Å / Num. obs: 34900 / % possible obs: 99.9 % / Observed criterion σ(I): 4.5 / Redundancy: 8.6 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.5 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2AR5, 2IWL,1O7K, 2V6V Resolution: 1.25→26.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.556 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / 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 mean: 9.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→26.71 Å
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Refine LS restraints |
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