+Open data
-Basic information
Entry | Database: PDB / ID: 5h78 | ||||||
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Title | Crystal structure of the PKA-DHR14 fusion protein | ||||||
Components | cAMP-dependent protein kinase type II-alpha regulatory subunit,DHR14 | ||||||
Keywords | SIGNALING PROTEIN / DE NOVO PROTEIN / synthetic protein | ||||||
Function / homology | Function and homology information ROBO receptors bind AKAP5 / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / plasma membrane raft ...ROBO receptors bind AKAP5 / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / plasma membrane raft / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / DARPP-32 events / Hedgehog 'off' state / cAMP binding / FCGR3A-mediated IL10 synthesis / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / intracellular signal transduction / protein domain specific binding / focal adhesion / centrosome / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å | ||||||
Authors | Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method. Authors: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h78.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h78.ent.gz | 138.8 KB | Display | PDB format |
PDBx/mmJSON format | 5h78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h78_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 5h78_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 5h78_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5h78_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/5h78 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/5h78 | HTTPS FTP |
-Related structure data
Related structure data | 5h75C 5h76C 5h77C 5h79C 5h7aC 5h7bC 5h7cC 5h7dC 5x3fC 5xbyC 2izxS 5cwhS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22333.561 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-40 (UNP RESIDUES 5-41),RESIDUES 41-196 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others) Gene: PRKAR2A, PKR2, PRKAR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13861 #2: Water | ChemComp-HOH / | |
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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: 3.91 Å3/Da / Density % sol: 68.51 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6.5 Details: 0.05M sodium cacodylate pH 6.5, 0.01M magnesium chloride, 0.2M potassium chloride, 12%(w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 83181 / % possible obs: 98.7 % / Redundancy: 3.5 % / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.21 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IZX, 5CWH Resolution: 2.002→29.593 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.52 Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.002→29.593 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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