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Yorodumi- PDB-1xlx: Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Ci... -
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-Basic information
Entry | Database: PDB / ID: 1xlx | ||||||
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Title | Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Cilomilast | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | ||||||
Keywords | HYDROLASE / PDE4B / Cilomilast | ||||||
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 / gamma-tubulin binding / regulation of cardiac muscle cell contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / leukocyte migration ...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 / gamma-tubulin binding / regulation of cardiac muscle cell contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / leukocyte migration / cAMP catabolic process / excitatory synapse / DARPP-32 events / 3',5'-cyclic-GMP phosphodiesterase activity / calcium channel regulator activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cAMP-mediated signaling / cellular response to epinephrine stimulus / neutrophil chemotaxis / positive regulation of interleukin-2 production / Z disc / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / synaptic vesicle / T cell receptor signaling pathway / cellular response to lipopolysaccharide / transmembrane transporter binding / dendritic spine / postsynaptic density / centrosome / perinuclear region of cytoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Card, G.L. / England, B.P. / Suzuki, Y. / Fong, D. / Powell, B. / Lee, B. / Luu, C. / Tabrizizad, M. / Gillette, S. / Ibrahim, P.N. ...Card, G.L. / England, B.P. / Suzuki, Y. / Fong, D. / Powell, B. / Lee, B. / Luu, C. / Tabrizizad, M. / Gillette, S. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Zhang, K.Y.J. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases. Authors: Card, G.L. / England, B.P. / Suzuki, Y. / Fong, D. / Powell, B. / Lee, B. / Luu, C. / Tabrizizad, M. / Gillette, S. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. / Milburn, M.V. / Kim, S.-H. / ...Authors: Card, G.L. / England, B.P. / Suzuki, Y. / Fong, D. / Powell, B. / Lee, B. / Luu, C. / Tabrizizad, M. / Gillette, S. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Zhang, K.Y.J. | ||||||
History |
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Remark 600 | HETEROGEN HOH 1003-1008 ARE ASSOCIATED WITH CHAIN A. HOH 2003-2008 ARE ASSOCIATED WITH CHAIN B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xlx.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xlx.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xlx_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1xlx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1xlx_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 1xlx_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/1xlx ftp://data.pdbj.org/pub/pdb/validation_reports/xl/1xlx | HTTPS FTP |
-Related structure data
Related structure data | 1xlzC 1xm4C 1xm6C 1xmuC 1xmyC 1xn0C 1xomC 1xonC 1xoqC 1xorC 1xosC 1xotC 1xozC 1xp0C 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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2 |
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Unit cell |
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Details | The biological assembly is one monomer. |
-Components
#1: Protein | Mass: 45731.332 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4B / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus(RIL) References: UniProt: Q07343, 3',5'-cyclic-nucleotide phosphodiesterase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.44 Å3/Da / Density % sol: 49.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10 Details: ammonium sulfate and lithium sulfate , pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→70.71 Å / Num. all: 41167 / Num. obs: 41167 / % possible obs: 92.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.19→2.247 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.1 / Num. unique all: 3048 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→70.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.688 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.276 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.326 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→70.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.247 Å / Total num. of bins used: 20
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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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