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- PDB-4ojx: crystal structure of yeast phosphodiesterase-1 in complex with GMP -

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Basic information

Entry
Database: PDB / ID: 4ojx
Titlecrystal structure of yeast phosphodiesterase-1 in complex with GMP
Components3',5'-cyclic-nucleotide phosphodiesterase 1
KeywordsHYDROLASE / phosphodiesterase / cGMP and cAMP / yeast PDE / dual specificity
Function / homology
Function and homology information


negative regulation of glucose mediated signaling pathway / 3',5'-cyclic-nucleotide phosphodiesterase / cAMP catabolic process / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity
Similarity search - Function
Cyclic-AMP phosphodiesterase, class-II / Cyclic-AMP phosphodiesterase class-II, conserved site / cAMP phosphodiesterases class-II / cAMP phosphodiesterases class-II signature. / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / 3',5'-cyclic-nucleotide phosphodiesterase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 Å
AuthorsTian, Y. / Cui, W. / Huang, M. / Robinson, H. / Wan, Y. / Wang, Y. / Ke, H.
CitationJournal: Biochemistry / Year: 2014
Title: Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate.
Authors: Tian, Y. / Cui, W. / Huang, M. / Robinson, H. / Wan, Y. / Wang, Y. / Ke, H.
History
DepositionJan 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 2.0Apr 20, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity_name_com / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3',5'-cyclic-nucleotide phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6825
Polymers42,0701
Non-polymers6124
Water3,873215
1
A: 3',5'-cyclic-nucleotide phosphodiesterase 1
hetero molecules

A: 3',5'-cyclic-nucleotide phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,36410
Polymers84,1402
Non-polymers1,2248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6620 Å2
ΔGint-62 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.674, 85.162, 130.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 3',5'-cyclic-nucleotide phosphodiesterase 1 / PDEase 1 / 3':5'-CNP / Low-affinity cAMP phosphodiesterase


Mass: 42070.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: PDE1, YGL248W, NRB369 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P22434, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The native crystal of yPDE1 (6 mg/ml) was grown by hanging drop against a buffer of 20 mM HEPES pH 7.5, 5% PEG3350, 40 mM Li sulfate, and 12% MPD at room temperature, or a similar buffer but ...Details: The native crystal of yPDE1 (6 mg/ml) was grown by hanging drop against a buffer of 20 mM HEPES pH 7.5, 5% PEG3350, 40 mM Li sulfate, and 12% MPD at room temperature, or a similar buffer but 15% glycerol and 20% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2013
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.31→34.34 Å / Num. all: 98268 / Num. obs: 98268 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.31→34.34 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.215 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17914 4910 5 %RANDOM
Rwork0.16806 ---
obs0.16864 93308 99.52 %-
all-98268 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.234 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.31→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 34 215 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023021
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9874087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91224.444135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.34415537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.111515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212242
X-RAY DIFFRACTIONr_rigid_bond_restr2.58833021
X-RAY DIFFRACTIONr_sphericity_free14.527560
X-RAY DIFFRACTIONr_sphericity_bonded6.21953103
LS refinement shellResolution: 1.31→1.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 317 -
Rwork0.302 6318 -
obs--95.58 %

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