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- PDB-3dyq: human phosphodiestrase 9 (inhibited by omitting divalent cation) ... -

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Basic information

Entry
Database: PDB / ID: 3dyq
Titlehuman phosphodiestrase 9 (inhibited by omitting divalent cation) in complex with cGMP
ComponentsHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
KeywordsHYDROLASE / PHOSPHODIESTERASE / ENZYME MECHANISM / cGMP / Manganese / Metal-binding / Phosphoprotein
Function / homology
Function and homology information


cGMP metabolic process / negative regulation of neural precursor cell proliferation / 3',5'-cyclic-GMP phosphodiesterase / calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / cGMP catabolic process / positive regulation of cardiac muscle hypertrophy / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity ...cGMP metabolic process / negative regulation of neural precursor cell proliferation / 3',5'-cyclic-GMP phosphodiesterase / calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / cGMP catabolic process / positive regulation of cardiac muscle hypertrophy / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / positive regulation of long-term synaptic potentiation / sarcolemma / ruffle membrane / perikaryon / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / signal transduction / nucleoplasm / metal ion binding / identical protein binding / plasma membrane / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-ISOBUTYL-1-METHYLXANTHINE / CYCLIC GUANOSINE MONOPHOSPHATE / High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsLiu, S. / Mansour, M.N. / Dillman, K. / Perez, J. / Danley, D. / Menniti, F.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural basis for the catalytic mechanism of human phosphodiesterase 9.
Authors: Liu, S. / Mansour, M.N. / Dillman, K.S. / Perez, J.R. / Danley, D.E. / Aeed, P.A. / Simons, S.P. / Lemotte, P.K. / Menniti, F.S.
History
DepositionJul 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 2023Group: 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_ncs_dom_lim / struct_ref_seq_dif / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
B: High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3858
Polymers77,7262
Non-polymers6596
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
hetero molecules

B: High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3858
Polymers77,7262
Non-polymers6596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z+1/41
Buried area3920 Å2
ΔGint-170 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.650, 103.650, 270.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLNGLNAA178 - 4271 - 250
21GLYGLYGLNGLNBB178 - 4271 - 250
12THRTHRASPASPAA448 - 488271 - 311
22THRTHRASPASPBB448 - 488271 - 311

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Components

#1: Protein High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A


Mass: 38862.926 Da / Num. of mol.: 2 / Fragment: Catalytic domain, UNP residues 242-566
Source method: isolated from a genetically manipulated source
Details: N-His tag (removed after purification) catalytic domain
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE9A / Production host: Escherichia coli (E. coli)
References: UniProt: O76083, 3',5'-cyclic-GMP phosphodiesterase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O7P
#4: Chemical ChemComp-IBM / 3-ISOBUTYL-1-METHYLXANTHINE


Mass: 222.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O2 / Comment: inhibitor, antagonist*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.66 Å3/Da / Density % sol: 73.58 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 65299 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 23

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Processing

SoftwareName: REFMAC / Version: 5.3.0008 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1TBM

1tbm
PDB Unreleased entry


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 14.204 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22627 5261 10.2 %RANDOM
Rwork0.19566 ---
obs0.19885 46414 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.023 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å20 Å2
2--1.86 Å20 Å2
3----3.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 43 238 5693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225595
X-RAY DIFFRACTIONr_bond_other_d0.0010.023816
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9637584
X-RAY DIFFRACTIONr_angle_other_deg0.83239298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99124.317278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.57151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6031532
X-RAY DIFFRACTIONr_chiral_restr0.0770.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026101
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021129
X-RAY DIFFRACTIONr_nbd_refined0.2620.21557
X-RAY DIFFRACTIONr_nbd_other0.2130.24053
X-RAY DIFFRACTIONr_nbtor_refined0.2010.22827
X-RAY DIFFRACTIONr_nbtor_other0.0920.22788
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2030.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.53300
X-RAY DIFFRACTIONr_mcbond_other0.1871.51288
X-RAY DIFFRACTIONr_mcangle_it1.49925380
X-RAY DIFFRACTIONr_scbond_it2.7632389
X-RAY DIFFRACTIONr_scangle_it4.3274.52204
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1723tight positional0.060.05
2334medium positional0.220.5
1723tight thermal0.160.5
2334medium thermal0.752
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 356 -
Rwork0.32 3396 -
obs--99.6 %
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)
11.0896-0.60360.02950.81950.00481.02270.0725-0.0468-0.0064-0.0179-0.02180.1042-0.0772-0.0207-0.05070.0097-0.0035-0.0158-0.19550.0097-0.056484.034145.641945.7999
20.5446-0.11950.2091.5557-0.50231.44450.0340.1404-0.0751-0.0676-0.0343-0.01750.18010.02690.0003-0.04930.03690.0001-0.0991-0.0196-0.056192.698831.90177.1034
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A181 - 505
2X-RAY DIFFRACTION2B181 - 505

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