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Yorodumi- PDB-5jix: PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jix | ||||||
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Title | PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP | ||||||
Components | cGMP-dependent protein kinase 2 | ||||||
Keywords | TRANSFERASE / Cyclic GMP-Dependent Protein Kinase Type II | ||||||
Function / homology | Function and homology information negative regulation of chloride transport / tetrahydrobiopterin metabolic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / positive regulation of chondrocyte differentiation / mitogen-activated protein kinase binding / positive regulation of protein localization / cGMP effects / cGMP binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation ...negative regulation of chloride transport / tetrahydrobiopterin metabolic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / positive regulation of chondrocyte differentiation / mitogen-activated protein kinase binding / positive regulation of protein localization / cGMP effects / cGMP binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / protein kinase A signaling / protein localization to plasma membrane / RAS processing / Ca2+ pathway / nuclear membrane / protein kinase activity / apical plasma membrane / protein phosphorylation / protein serine kinase activity / signal transduction / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Campbell, J.C. / Kim, C.W. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Structural Basis of Analog Specificity in PKG I and II. Authors: Campbell, J.C. / Henning, P. / Franz, E. / Sankaran, B. / Herberg, F.W. / Kim, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jix.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jix.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jix_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5jix_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5jix_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 5jix_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/5jix ftp://data.pdbj.org/pub/pdb/validation_reports/ji/5jix | HTTPS FTP |
-Related structure data
Related structure data | 5j48C 5jaxC 5jd7C 5bv6S S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17394.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG2, PRKGR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13237, cGMP-dependent protein kinase |
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-Non-polymers , 6 types, 131 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PE5 / | #5: Chemical | ChemComp-6J7 / | #6: Chemical | ChemComp-NA / | #7: 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: 2.14 Å3/Da / Density % sol: 42.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 400, 200 mM CaAc, 0.1M NaAc pH 4.5-4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→41.494 Å / Num. obs: 25594 / % possible obs: 98.17 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5bv6 Resolution: 1.47→41.494 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.47→41.494 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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