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Yorodumi- PDB-1k8f: CRYSTAL STRUCTURE OF THE HUMAN C-TERMINAL CAP1-ADENYLYL CYCLASE A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k8f | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN C-TERMINAL CAP1-ADENYLYL CYCLASE ASSOCIATED PROTEIN | ||||||
Components | ADENYLYL CYCLASE-ASSOCIATED PROTEIN | ||||||
Keywords | UNKNOWN FUNCTION / CAP / CAP1 / ADENYLYL CYCLASE ASSOCIATED PROTEIN / ACTIN BINDING / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information regulation of adenylate cyclase activity / ameboidal-type cell migration / neutrophil degranulation / Role of ABL in ROBO-SLIT signaling / actin polymerization or depolymerization / establishment or maintenance of cell polarity / cortical actin cytoskeleton / activation of adenylate cyclase activity / adenylate cyclase binding / receptor-mediated endocytosis ...regulation of adenylate cyclase activity / ameboidal-type cell migration / neutrophil degranulation / Role of ABL in ROBO-SLIT signaling / actin polymerization or depolymerization / establishment or maintenance of cell polarity / cortical actin cytoskeleton / activation of adenylate cyclase activity / adenylate cyclase binding / receptor-mediated endocytosis / cell morphogenesis / azurophil granule lumen / Platelet degranulation / actin binding / focal adhesion / Neutrophil degranulation / signal transduction / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Patskovsky, Y.V. / Chance, M. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal structure of the actin binding domain of the cyclase-associated protein. Authors: Dodatko, T. / Fedorov, A.A. / Grynberg, M. / Patskovsky, Y. / Rozwarski, D.A. / Jaroszewski, L. / Aronoff-Spencer, E. / Kondraskina, E. / Irving, T. / Godzik, A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k8f.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k8f.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k8f_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 1k8f_full_validation.pdf.gz | 471.2 KB | Display | |
Data in XML | 1k8f_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 1k8f_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8f ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8f | HTTPS FTP |
-Related structure data
Related structure data | 1k4zSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17361.912 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAP1 / Plasmid: PCRTOPO-NT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01518 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl, pH 8.5, 27.5% PEG4000, 0.2M NaOAc, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 83 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 16, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 16727 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 9.06 % / Rmerge(I) obs: 0.059 / Rsym value: 0.054 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 6.3 / Rsym value: 0.154 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K4Z Resolution: 2.8→10 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0.001 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO |