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- PDB-3dyl: human phosphdiesterase 9 substrate complex (ES complex) -

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Basic information

Entry
Database: PDB / ID: 3dyl
Titlehuman phosphdiesterase 9 substrate complex (ES complex)
Componentshuman phosphodiesterase 9
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 / positive regulation of cardiac muscle hypertrophy / cGMP catabolic process / cGMP effects / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-nucleotide 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-GMP phosphodiesterase activity / 3',5'-cyclic-nucleotide 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
FORMIC ACID / 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 / FOURIER SYNTHESIS / Resolution: 2.7 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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

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Assembly

Deposited unit
A: human phosphodiesterase 9
B: human phosphodiesterase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4989
Polymers77,7262
Non-polymers7727
Water3,189177
1
A: human phosphodiesterase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2874
Polymers38,8631
Non-polymers4243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: human phosphodiesterase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2105
Polymers38,8631
Non-polymers3484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.787, 103.787, 269.799
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 human phosphodiesterase 9 /


Mass: 38862.926 Da / Num. of mol.: 2 / Fragment: Catalytic domain, UNP residues 242-566
Source method: isolated from a genetically manipulated source
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 , 6 types, 184 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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.: 1 / 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: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 4.67 Å3/Da / Density % sol: 73.68 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Site: APS / Beamline: 17-ID / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→96.67 Å / Num. all: 37247 / Num. obs: 37247 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2 / Num. unique all: 4075 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.3.0008 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→96.67 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 16.892 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21902 4216 10.2 %RANDOM
Rwork0.18757 ---
obs0.19089 37247 99.72 %-
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: 42.135 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2--2.06 Å20 Å2
3----4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.7→96.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 46 177 5635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225597
X-RAY DIFFRACTIONr_bond_other_d0.0020.023816
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9637585
X-RAY DIFFRACTIONr_angle_other_deg1.11839298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0555654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57624.317278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.289151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1171532
X-RAY DIFFRACTIONr_chiral_restr0.1060.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026102
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021127
X-RAY DIFFRACTIONr_nbd_refined0.2530.21495
X-RAY DIFFRACTIONr_nbd_other0.20.23979
X-RAY DIFFRACTIONr_nbtor_refined0.2020.22786
X-RAY DIFFRACTIONr_nbtor_other0.0960.22831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1690.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0861.54212
X-RAY DIFFRACTIONr_mcbond_other0.1861.51288
X-RAY DIFFRACTIONr_mcangle_it1.26225381
X-RAY DIFFRACTIONr_scbond_it2.31832697
X-RAY DIFFRACTIONr_scangle_it3.4214.52204
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 positional0.050.05
B2000medium positional0.070.5
A1479tight thermal0.140.5
B2000medium thermal0.172
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 278 -
Rwork0.319 2712 -
obs--99.47 %
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)
11.5919-0.7891-0.14491.6376-0.08471.82470.086-0.05010.02670.1079-0.05340.1049-0.16-0.02-0.0326-0.0673-0.0231-0.0159-0.2917-0.0017-0.140684.293145.50445.8341
21.1757-0.35240.4522.0968-0.43141.94320.04120.2439-0.071-0.1142-0.049-0.03470.12540.1150.0078-0.15470.04710.0199-0.1619-0.0109-0.141892.62531.80787.0866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A181 - 505
2X-RAY DIFFRACTION2B181 - 505

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