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Yorodumi- PDB-5e16: Co-crystal structure of the N-termial cGMP binding domain of Plas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+16 | ||||||
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Title | Co-crystal structure of the N-termial cGMP binding domain of Plasmodium falciparum PKG with cGMP | ||||||
Components | CGMP-dependent protein kinase | ||||||
Keywords | TRANSFERASE / Kinase / cGMP binding domain / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / HDL assembly / : / : / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / : / : / : / MAPK6/MAPK4 signaling ...Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / HDL assembly / : / : / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / : / : / : / MAPK6/MAPK4 signaling / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / gamete generation / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / extrinsic component of membrane / cGMP binding / protein phosphorylation / protein serine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / signal transduction / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | El Bakkouri, M. / Walker, J.R. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Structures of the cGMP-dependent protein kinase in malaria parasites reveal a unique structural relay mechanism for activation. Authors: El Bakkouri, M. / Kouidmi, I. / Wernimont, A.K. / Amani, M. / Hutchinson, A. / Loppnau, P. / Kim, J.J. / Flueck, C. / Walker, J.R. / Seitova, A. / Senisterra, G. / Kakihara, Y. / Kim, C. / ...Authors: El Bakkouri, M. / Kouidmi, I. / Wernimont, A.K. / Amani, M. / Hutchinson, A. / Loppnau, P. / Kim, J.J. / Flueck, C. / Walker, J.R. / Seitova, A. / Senisterra, G. / Kakihara, Y. / Kim, C. / Blackman, M.J. / Calmettes, C. / Baker, D.A. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e16.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e16.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 5e16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/5e16 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/5e16 | HTTPS FTP |
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-Related structure data
Related structure data | 5dykC 5dylC 5dzcC 4myj 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
#1: Protein | Mass: 16078.078 Da / Num. of mol.: 1 / Fragment: cGMP binding domain (UNP residues 21-162) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8MMZ4, UniProt: Q8I719*PLUS |
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#2: Chemical | ChemComp-PCG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25 % Peg3350, 0.2 M NaCl, 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 2, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 15745 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Χ2: 1.587 / Net I/av σ(I): 59.607 / Net I/σ(I): 19.4 / Num. measured all: 116330 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MYJ 4myj Resolution: 1.65→46.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.358 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.65 Å2 / Biso mean: 27.091 Å2 / Biso min: 14.96 Å2
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Refinement step | Cycle: final / Resolution: 1.65→46.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.649→1.692 Å / Total num. of bins used: 20
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