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- PDB-3dyn: human phosphodiestrase 9 in complex with cGMP (Zn inhibited) -

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Basic information

Entry
Database: PDB / ID: 3dyn
Titlehuman phosphodiestrase 9 in complex with cGMP (Zn inhibited)
ComponentsHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
KeywordsHYDROLASE / phophodiestrase / 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 / positive regulation of cardiac muscle hypertrophy / cGMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / positive regulation of long-term synaptic potentiation / sarcolemma ...cGMP metabolic process / negative regulation of neural precursor cell proliferation / 3',5'-cyclic-GMP phosphodiesterase / positive regulation of cardiac muscle hypertrophy / cGMP catabolic process / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / positive regulation of long-term synaptic potentiation / sarcolemma / ruffle membrane / perikaryon / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / nucleoplasm / identical protein binding / metal ion 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: 2.1 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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)78,8189
Polymers77,7262
Non-polymers1,0927
Water8,107450
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A: High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2984
Polymers38,8631
Non-polymers4353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5205
Polymers38,8631
Non-polymers6574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.857, 103.857, 270.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain: (Details: A B)

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Components

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Protein , 1 types, 2 molecules AB

#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) catalytic domain / Source: (gene. exp.) Homo sapiens (human) / Gene: PDE9A / Production host: Escherichia coli (E. coli)
References: UniProt: O76083, 3',5'-cyclic-GMP phosphodiesterase

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Non-polymers , 5 types, 457 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P
#5: Chemical ChemComp-IBM / 3-ISOBUTYL-1-METHYLXANTHINE / IBMX


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


Mass: 18.015 Da / Num. of mol.: 450 / 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: 4.69 Å3/Da / Density % sol: 73.75 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 87053 / Num. obs: 77963 / % possible obs: 99.82 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.1

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Processing

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

1tbm
PDB Unreleased entry


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.496 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20274 8759 10.1 %RANDOM
Rwork0.18017 ---
obs0.18251 77963 99.82 %-
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: 31.797 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 66 450 5928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225621
X-RAY DIFFRACTIONr_bond_other_d0.0010.023822
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9687625
X-RAY DIFFRACTIONr_angle_other_deg0.80739316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40324.317278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9591532
X-RAY DIFFRACTIONr_chiral_restr0.0770.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026145
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021127
X-RAY DIFFRACTIONr_nbd_refined0.2380.21369
X-RAY DIFFRACTIONr_nbd_other0.2170.24007
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22773
X-RAY DIFFRACTIONr_nbtor_other0.0910.22714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1711.54307
X-RAY DIFFRACTIONr_mcbond_other0.441.51288
X-RAY DIFFRACTIONr_mcangle_it2.36225380
X-RAY DIFFRACTIONr_scbond_it4.26232710
X-RAY DIFFRACTIONr_scangle_it6.1334.52245
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1479tight positional0.060.05
B2000medium positional0.10.5
A1479tight thermal0.310.5
B2000medium thermal0.332
LS refinement shellResolution: 2.1→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 632 -
Rwork0.28 5595 -
obs--98.31 %
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)
10.3748-0.3538-0.050.41810.05310.5430.0746-0.0359-0.0322-0.0264-0.00640.0513-0.05890.0491-0.06820.0427-0.0132-0.0147-0.12110.0118-0.013184.259145.687145.7531
20.1857-0.13860.0710.6893-0.28080.79490.01750.0919-0.01640.0012-0.0267-0.01170.06870.02790.0092-0.00660.04130.002-0.0426-0.0099-0.011692.820532.05386.945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A181 - 505
2X-RAY DIFFRACTION2B181 - 505

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