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Yorodumi- PDB-3ocp: Crystal structure of cAMP bound cGMP-dependent protein kinase(92-227) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ocp | ||||||
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Title | Crystal structure of cAMP bound cGMP-dependent protein kinase(92-227) | ||||||
Components | PRKG1 protein | ||||||
Keywords | TRANSFERASE / serine/threonine kinase / TF2I and IRAG | ||||||
Function / homology | Function and homology information negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm ...negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / negative regulation of vascular associated smooth muscle cell proliferation / mitogen-activated protein kinase p38 binding / regulation of GTPase activity / cGMP-mediated signaling / dendrite development / cGMP effects / spermatid development / calcium channel regulator activity / cGMP binding / forebrain development / protein kinase A signaling / cerebellum development / acrosomal vesicle / neuron migration / sarcolemma / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Kim, J.J. / Huang, G. / Kwon, T.K. / Zwart, P. / Headd, J. / Kim, C. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Co-Crystal Structures of PKG Ibeta (92-227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding Authors: Kim, J.J. / Casteel, D.E. / Huang, G. / Kwon, T.H. / Ren, R.K. / Zwart, P. / Headd, J.J. / Brown, N.G. / Chow, D.C. / Palzkill, T. / Kim, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ocp.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ocp.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ocp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ocp_validation.pdf.gz | 1021.8 KB | Display | wwPDB validaton report |
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Full document | 3ocp_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3ocp_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3ocp_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/3ocp ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3ocp | HTTPS FTP |
-Related structure data
Related structure data | 3od0C 3ogjC 1rgsS 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
#1: Protein | Mass: 15607.178 Da / Num. of mol.: 2 / Fragment: Cyclic nucleotie binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6P5T7, UniProt: Q13976*PLUS, cGMP-dependent protein kinase #2: Chemical | #3: 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: 4.48 Å3/Da / Density % sol: 72.57 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.4 M sodium/potassium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2009 |
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. all: 20607 / Num. obs: 20339 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.8 % / Rmerge(I) obs: 0.105 / Rsym value: 0.101 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RGS Resolution: 2.49→46.393 Å / SU ML: 0.27 / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.374 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.49→46.393 Å
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Refine LS restraints |
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LS refinement shell |
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