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- PDB-1mc0: Regulatory Segment of Mouse 3',5'-Cyclic Nucleotide Phosphodieste... -

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Basic information

Entry
Database: PDB / ID: 1mc0
TitleRegulatory Segment of Mouse 3',5'-Cyclic Nucleotide Phosphodiesterase 2A, Containing the GAF A and GAF B Domains
Components3',5'-cyclic nucleotide phosphodiesterase 2A
KeywordsHYDROLASE / GAF DOMAIN / 3' / 5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE / 5'-GUANOSINE MONOPHOSPHATE
Function / homology
Function and homology information


hippocampal mossy fiber / cGMP effects / GAF domain binding / : / cellular response to xenobiotic stimulus => GO:0071466 / : / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / G alpha (s) signalling events / cellular response to macrophage colony-stimulating factor stimulus / cardiac septum development ...hippocampal mossy fiber / cGMP effects / GAF domain binding / : / cellular response to xenobiotic stimulus => GO:0071466 / : / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / G alpha (s) signalling events / cellular response to macrophage colony-stimulating factor stimulus / cardiac septum development / regulation of nitric oxide mediated signal transduction / cellular response to cGMP / positive regulation of vascular permeability / heart valve development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / coronary vasculature development / negative regulation of oxidative phosphorylation / negative regulation of vascular permeability / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / regulation of mitochondrion organization / aorta development / ventricular septum development / cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP-mediated signaling / TPR domain binding / cGMP catabolic process / phosphate ion binding / 3',5'-cyclic-GMP phosphodiesterase activity / cAMP-mediated signaling / cGMP binding / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cellular response to cAMP / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / synaptic membrane / positive regulation of inflammatory response / cellular response to mechanical stimulus / presynaptic membrane / heart development / cellular response to lipopolysaccharide / mitochondrial inner membrane / mitochondrial outer membrane / mitochondrial matrix / membrane raft / axon / dendrite / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / mitochondrion / zinc ion binding / nucleus / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GAF domain / GAF domain / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 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. ...GAF domain / GAF domain / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 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 / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CYCLIC GUANOSINE MONOPHOSPHATE / cGMP-dependent 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.86 Å
AuthorsMartinez, S. / Wu, A. / Glavas, N. / Tang, X. / Turley, S. / Hol, W. / Beavo, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding.
Authors: Martinez, S.E. / Wu, A.Y. / Glavas, N.A. / Tang, X.B. / Turley, S. / Hol, W.G. / Beavo, J.A.
History
DepositionAug 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3',5'-cyclic nucleotide phosphodiesterase 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7692
Polymers41,4241
Non-polymers3451
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit in distinct coordinate
  • defined by author
TypeNameSymmetry operationNumber
crystal symmetry operation14_655-x+3/2,-y+1/2,z1
3
A: 3',5'-cyclic nucleotide phosphodiesterase 2A
hetero molecules

A: 3',5'-cyclic nucleotide phosphodiesterase 2A
hetero molecules

A: 3',5'-cyclic nucleotide phosphodiesterase 2A
hetero molecules

A: 3',5'-cyclic nucleotide phosphodiesterase 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,0768
Polymers165,6964
Non-polymers1,3814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x,-y+1/2,-z+3/21
crystal symmetry operation11_656-x+3/2,y,-z+3/21
crystal symmetry operation14_655-x+3/2,-y+1/2,z1
Buried area16900 Å2
ΔGint-124 kcal/mol
Surface area61310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)134.200, 136.200, 149.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein 3',5'-cyclic nucleotide phosphodiesterase 2A


Mass: 41423.910 Da / Num. of mol.: 1 / Fragment: Regulatory domain (residues 207-566) / Mutation: Y230F, F389L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: PDE2A
Plasmid details: pRUNH is a derivative of pMW172. Way, M., Pope, B., Gooch, J., Hawkins, M. & Weeds, A. G. (1990) Embo J 9, 4103-9
Plasmid: pRUNH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q922S4, 3',5'-cyclic-GMP phosphodiesterase
#2: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE / Cyclic guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 4.11 Å3/Da / Density % sol: 70.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1,4 butanediol, sodium acetate, dithiothreitol, EDTA, Tris, sodium chloride, 3',5' guanosine monophosphate, leupeptin, pepstatin, phenylmethylsulfonyl flouride, pH 5.0, VAPOR DIFFUSION, ...Details: 1,4 butanediol, sodium acetate, dithiothreitol, EDTA, Tris, sodium chloride, 3',5' guanosine monophosphate, leupeptin, pepstatin, phenylmethylsulfonyl flouride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12-5 mg/mlprotein1drop
220 mM1dropNaCl
310 mMTris1droppH7.5
410 mMdithiothreitol1drop
50.1 mMEDTA1drop
60.1 mMPMSF1drop
70.001 mg/mlleupeptin1drop
80.001 mg/mlpepstain A1drop
92 mMNa 3',5'cGMP1drop
1016-26 %1,4butanediol1reservoir
11100 mMsodium acetate1reservoirpH5.0
12140 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.86→19.97 Å / Num. all: 15282 / Num. obs: 15282 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.058
Reflection shellResolution: 2.86→2.97 Å / Num. unique all: 1380 / Rsym value: 0.408 / % possible all: 87.2
Reflection
*PLUS
Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 87.2 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.86→19.97 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1838569.21 / Data cutoff high rms absF: 1838569.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 756 4.9 %RANDOM
Rwork0.221 ---
obs0.221 15282 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.1207 Å2 / ksol: 0.291099 e/Å3
Displacement parametersBiso mean: 89 Å2
Baniso -1Baniso -2Baniso -3
1--15.96 Å20 Å20 Å2
2--41.76 Å20 Å2
3----25.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.86→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 23 38 2727
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it3.022
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.86→2.96 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.459 61 4.5 %
Rwork0.388 1287 -
obs-1348 85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PCG_PAR.TXTWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMPCG_TOP.TXT
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.221 / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.459 / Rfactor Rwork: 0.388

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