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- PDB-3itm: Catalytic domain of hPDE2A -

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Basic information

Entry
Database: PDB / ID: 3itm
TitleCatalytic domain of hPDE2A
ComponentscGMP-dependent 3',5'-cyclic phosphodiesterase
KeywordsHYDROLASE / ZN-binding / All-ALPHA HELICAL / cGMP / Membrane
Function / homology
Function and homology information


: / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / heart valve development / positive regulation of vascular permeability / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier ...: / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / heart valve development / positive regulation of vascular permeability / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier / regulation of mitochondrion organization / : / 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / aorta development / ventricular septum development / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of receptor guanylyl cyclase signaling pathway / cGMP catabolic process / cGMP effects / phosphate ion binding / TPR domain binding / cGMP binding / monocyte differentiation / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cellular response to transforming growth factor beta stimulus / : / cAMP binding / synaptic membrane / cellular response to cAMP / cellular response to mechanical stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cellular response to xenobiotic stimulus / positive regulation of inflammatory response / presynaptic membrane / G alpha (s) signalling events / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein homodimerization activity / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / 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. / GAF domain ...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. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / GAF-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
cGMP-dependent 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsPandit, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct.
Authors: Pandit, J. / Forman, M.D. / Fennell, K.F. / Dillman, K.S. / Menniti, F.S.
History
DepositionAug 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,1628
Polymers160,9004
Non-polymers2624
Water2,936163
1
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2912
Polymers40,2251
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2912
Polymers40,2251
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2912
Polymers40,2251
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2912
Polymers40,2251
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5814
Polymers80,4502
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-16 kcal/mol
Surface area27450 Å2
MethodPISA
6
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5814
Polymers80,4502
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-20 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.017, 108.017, 515.563
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11D-90-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 2 / Auth seq-ID: 588 - 896 / Label seq-ID: 14 - 322

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
cGMP-dependent 3',5'-cyclic phosphodiesterase / Cyclic GMP-stimulated phosphodiesterase / CGS-PDE / cGSPDE


Mass: 40225.102 Da / Num. of mol.: 4 / Fragment: catalytic domain, residues 579-919
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE2A, PDE2A 579-919 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O00408, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Reservoir - 20% PDEG 3350, 0.2M tri-sodium citrate. Protein - 25mM Hepes pH7.5, 25mM NaCl, 2mM TCEP, 10ug/mL E-64, 1ug/mL pepstatin., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 64064 / Num. obs: 54006 / % possible obs: 84.3 % / Observed criterion σ(I): -3 / Redundancy: 6.52 % / Rsym value: 0.089 / Net I/σ(I): 19.36
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.19 / Rsym value: 0.318 / % possible all: 38.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.886 / SU B: 22.86 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.641 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28648 2756 5.1 %RANDOM
Rwork0.22686 ---
obs0.22982 51187 84.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10280 0 4 163 10447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.02110523
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.94614188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7451243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05223.783526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.245151906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1531562
X-RAY DIFFRACTIONr_chiral_restr0.140.21532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027930
X-RAY DIFFRACTIONr_nbd_refined0.2460.25193
X-RAY DIFFRACTIONr_nbtor_refined0.3230.27203
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2313
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.28
X-RAY DIFFRACTIONr_mcbond_it0.6891.56409
X-RAY DIFFRACTIONr_mcangle_it1.058210095
X-RAY DIFFRACTIONr_scbond_it2.14434648
X-RAY DIFFRACTIONr_scangle_it3.134.54093
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1204tight positional0.090.05
2B1204tight positional0.080.05
3C1204tight positional0.090.05
4D1204tight positional0.080.05
1A1265medium positional0.660.5
2B1265medium positional0.720.5
3C1265medium positional0.790.5
4D1265medium positional0.770.5
1A1204tight thermal0.210.5
2B1204tight thermal0.180.5
3C1204tight thermal0.170.5
4D1204tight thermal0.150.5
1A1265medium thermal1.242
2B1265medium thermal1.142
3C1265medium thermal1.082
4D1265medium thermal1.042
LS refinement shellResolution: 2.491→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 75 -
Rwork0.33 1591 -
obs--36.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2396-0.15380.61812.5335-0.74483.60160.00130.37920.0775-0.26720.0408-0.0634-0.03030.2581-0.0422-0.09210.0631-0.0409-0.0737-0.0012-0.360517.831-18.98914.581
21.91630.53950.61382.28970.23563.8830.043-0.15620.09710.4245-0.00120.0777-0.23660.1408-0.0417-0.0436-0.0549-0.0223-0.12920.0423-0.3286-11.139-21.361-19.622
32.4723-0.4612-0.16234.19660.18423.6244-0.0041-0.2055-0.2625-0.1050.17930.67150.1314-0.7181-0.1752-0.1578-0.0246-0.09290.12230.1462-0.1412-1.814-52.37121.831
42.63120.59880.62912.93410.41996.50050.16220.4679-0.33760.05610.1766-0.57750.196-0.0532-0.3388-0.12050.0856-0.09980.1238-0.0716-0.09499.002-54.765-22.411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A588 - 901
2X-RAY DIFFRACTION2B579 - 899
3X-RAY DIFFRACTION3C579 - 896
4X-RAY DIFFRACTION4D579 - 899

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