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Yorodumi- PDB-4x0f: Crystal structure of crosslink stabilized long-form PDE4B in comp... -
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-Basic information
Entry | Database: PDB / ID: 4x0f | ||||||
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Title | Crystal structure of crosslink stabilized long-form PDE4B in complex with (R)-(-)-rolipram | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | ||||||
Keywords | hydrolase/hydrolase inhibitor / phosphodiesterase / inhibitor / complex / HYDROLASE / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / regulation of cardiac muscle cell contraction / gamma-tubulin binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / leukocyte migration / voltage-gated calcium channel complex ...negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / regulation of cardiac muscle cell contraction / gamma-tubulin binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / leukocyte migration / voltage-gated calcium channel complex / cAMP catabolic process / calcium channel regulator activity / excitatory synapse / 3',5'-cyclic-AMP phosphodiesterase activity / DARPP-32 events / cAMP binding / cellular response to epinephrine stimulus / positive regulation of interleukin-2 production / neutrophil chemotaxis / Z disc / positive regulation of type II interferon production / synaptic vesicle / cellular response to xenobiotic stimulus / T cell receptor signaling pathway / cellular response to lipopolysaccharide / transmembrane transporter binding / dendritic spine / postsynaptic density / centrosome / perinuclear region of cytoplasm / signal transduction / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.22 Å | ||||||
Authors | Cedervall, P. / Pandit, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4. Authors: Cedervall, P. / Aulabaugh, A. / Geoghegan, K.F. / McLellan, T.J. / Pandit, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x0f.cif.gz | 355.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x0f.ent.gz | 287.7 KB | Display | PDB format |
PDBx/mmJSON format | 4x0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/4x0f ftp://data.pdbj.org/pub/pdb/validation_reports/x0/4x0f | HTTPS FTP |
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-Related structure data
Related structure data | 4wziSC 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: 74791.398 Da / Num. of mol.: 2 / Fragment: unp residues 122-736 Mutation: S133A, C229A, S267C, C366A, C492A, C562A, C604A, S610C, S654A, S659A, S661A, C671A, C709A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4B, DPDE4 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q07343, 3',5'-cyclic-AMP phosphodiesterase #2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 20% PEG 3350, 0.2M potassium iodide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.22→119 Å / Num. obs: 23686 / % possible obs: 91.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 65.44 Å2 / Rmerge(I) obs: 0.178 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.22→3.23 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.5 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4WZI Resolution: 3.22→119 Å / Cor.coef. Fo:Fc: 0.9196 / Cor.coef. Fo:Fc free: 0.8877 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.381
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Displacement parameters | Biso mean: 74.19 Å2
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Refine analyze | Luzzati coordinate error obs: 0.632 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.22→119 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.22→3.36 Å / Total num. of bins used: 12
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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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