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- PDB-3ecn: Crystal structure of PDE8A catalytic domain in complex with IBMX -

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Basic information

Entry
Database: PDB / ID: 3ecn
TitleCrystal structure of PDE8A catalytic domain in complex with IBMX
ComponentsHigh affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A
KeywordsHYDROLASE / IBMX / PDE8A catalytic domain / refolding / Alternative splicing / cAMP / Magnesium / Manganese / Metal-binding
Function / homology
Function and homology information


3',5'-cyclic-AMP phosphodiesterase / protein kinase activator activity / cAMP catabolic process / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cellular response to epidermal growth factor stimulus / kinase binding / G alpha (s) signalling events / positive regulation of ERK1 and ERK2 cascade / regulation of DNA-templated transcription ...3',5'-cyclic-AMP phosphodiesterase / protein kinase activator activity / cAMP catabolic process / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cellular response to epidermal growth factor stimulus / kinase binding / G alpha (s) signalling events / positive regulation of ERK1 and ERK2 cascade / regulation of DNA-templated transcription / signal transduction / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / PAS fold / PAS fold / PAS repeat profile. / PAS domain / PAS domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-ISOBUTYL-1-METHYLXANTHINE / High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsWang, H. / Yan, Z. / Yang, S. / Cai, J. / Robinson, H. / Ke, H.
CitationJournal: Biochemistry / Year: 2008
Title: Kinetic and structural studies of phosphodiesterase-8A and implication on the inhibitor selectivity
Authors: Wang, H. / Yan, Z. / Yang, S. / Cai, J. / Robinson, H. / Ke, H.
History
DepositionSep 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A
B: High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8048
Polymers78,1802
Non-polymers6246
Water2,414134
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A: High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4024
Polymers39,0901
Non-polymers3123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4024
Polymers39,0901
Non-polymers3123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.325, 101.601, 76.573
Angle α, β, γ (deg.)90.00, 119.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A


Mass: 39090.020 Da / Num. of mol.: 2 / Fragment: catalytic domain of PDE8A1 (UNP residues 482-819)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE8A / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O60658, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-IBM / 3-ISOBUTYL-1-METHYLXANTHINE / IBMX


Mass: 222.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O2 / Comment: inhibitor, antagonist*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: well buffer of 100 mM Na cacodylate, pH 6.5, 15% isopropanol, 30% ethylene glycol, 8% PEG3350 at 4oC, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 52808 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.23 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.9 / % possible all: 59.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: the unliganded PDE8A

Resolution: 2.1→30 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 5304 -random
Rwork0.221 ---
obs-52075 88.1 %-
Displacement parametersBiso mean: 50.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 36 134 5658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1

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