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Yorodumi- PDB-1kq5: C-terminal Domain of Cyclase Associated Protein with PRO 505 Repl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kq5 | ||||||
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Title | C-terminal Domain of Cyclase Associated Protein with PRO 505 Replaced by SER (P505S) | ||||||
Components | Adenylyl cyclase-associated protein | ||||||
Keywords | SIGNALING PROTEIN / Right-handed parallel beta-helix / intertwined dimer / actin-binding | ||||||
Function / homology | Function and homology information positive regulation of actin filament depolymerization / actin cortical patch / regulation of actin filament polymerization / actin filament severing / mating projection tip / actin filament depolymerization / positive regulation of Ras protein signal transduction / positive regulation of mitochondrial fission / adenylate cyclase binding / Neutrophil degranulation ...positive regulation of actin filament depolymerization / actin cortical patch / regulation of actin filament polymerization / actin filament severing / mating projection tip / actin filament depolymerization / positive regulation of Ras protein signal transduction / positive regulation of mitochondrial fission / adenylate cyclase binding / Neutrophil degranulation / cAMP-mediated signaling / actin filament organization / cell morphogenesis / actin binding / Ras protein signal transduction / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Fedorov, A.A. / Dodatko, T. / Roswarski, D.A. / Almo, S.C. | ||||||
Citation | Journal: To be Published Title: Mutant Structures of the Actin-binding Domain of Cyclase Associated Protein (CAP) from Saccharomyces Cerevisiae Authors: Fedorov, A.A. / Dodatko, T. / Roswarski, D.A. / Almo, S.C. #1: Journal: J.Biol.Chem. / Year: 1996 Title: Two separate functions are encoded by the carboxyl-terminal domains of the yeast cyclase-associated protein and its mammalian homologs. Dimerization and actin binding. Authors: Zelicof, A. / Protopopov, V. / David, D. / Lin, X.Y. / Lusgarten, V. / Gerst, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kq5.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kq5.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 1kq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kq5_validation.pdf.gz | 372.8 KB | Display | wwPDB validaton report |
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Full document | 1kq5_full_validation.pdf.gz | 379.5 KB | Display | |
Data in XML | 1kq5_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1kq5_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/1kq5 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/1kq5 | HTTPS FTP |
-Related structure data
Related structure data | 1k4zS 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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3 |
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4 |
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Unit cell |
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Details | The biological assembly is a monomer generated from monomer A or from monomer B in the asymmetric unit |
-Components
#1: Protein | Mass: 17530.604 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Mutation: P505S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P17555 |
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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: 2.82 Å3/Da / Density % sol: 56.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, lithium sulfate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.04 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 3→10 Å / Num. all: 7755 / Num. obs: 7755 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 34.6 |
Reflection shell | Resolution: 3→3.19 Å / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 12.2 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K4Z Resolution: 3→10 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 40.8 Å2 / ksol: 0.4069 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.3 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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