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- PDB-2zmf: Crystal structure of the C-terminal GAF domain of human phosphodi... -

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Basic information

Entry
Database: PDB / ID: 2zmf
TitleCrystal structure of the C-terminal GAF domain of human phosphodiesterase 10A
ComponentscAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
KeywordsHYDROLASE / GAF domain / phosphodiesterase / cAMP / cGMP / cGMP-binding / Nucleotide-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cGMP effects / cAMP catabolic process / 3',5'-cyclic-GMP phosphodiesterase activity / cGMP binding / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity ...cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cGMP effects / cAMP catabolic process / 3',5'-cyclic-GMP phosphodiesterase activity / cGMP binding / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / G alpha (s) signalling events / signal transduction / metal ion binding / cytosol
Similarity search - Function
GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / GAF domain / 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. / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / GAF domain / 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. / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsHanda, N. / Kishishita, S. / Mizohata, E. / Omori, K. / Kotera, J. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of the GAF-B Domain from Human Phosphodiesterase 10A Complexed with Its Ligand, cAMP
Authors: Handa, N. / Mizohata, E. / Kishishita, S. / Toyama, M. / Morita, S. / Uchikubo-Kamo, T. / Akasaka, R. / Omori, K. / Kotera, J. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 17, 2008Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 29, 2008ID: 2E4S
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
B: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6124
Polymers42,9532
Non-polymers6582
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-37 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.506, 74.506, 146.524
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A


Mass: 21476.734 Da / Num. of mol.: 2 / Fragment: C-terminal GAF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE10A / Plasmid: PX060608-01 / Production host: cell free (Escherichia coli)
References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Ammonium sulfate, PEG, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9790, 0.9793, 0.9640
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2006 / Details: mirror
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.9641
ReflectionResolution: 2.1→50 Å / Num. obs: 28345 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.882 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.082 / Net I/σ(I): 21.1476
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 4.223 / Rsym value: 0.351 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→48.84 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.815 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22529 1431 5.1 %RANDOM
Rwork0.19859 ---
obs0.1999 26868 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 44 168 2992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222889
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9733907
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022156
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21283
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.941.51739
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69722812
X-RAY DIFFRACTIONr_scbond_it3.10831150
X-RAY DIFFRACTIONr_scangle_it4.4034.51095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 102
Rwork0.199 1923
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)
120.6973-22.025523.791224.0296-9.802610.9577-0.7837-0.2620.95481.4944-0.3002-1.35320.09880.55761.08380.2981-0.11330.02990.36240.07750.19122.122528.951375.4072
23.4728-0.37-1.69762.00821.06422.87650.18750.02680.70170.20980.07210.0516-0.4364-0.1661-0.25960.1480.03950.10470.16540.08110.243-0.436732.262458.3823
36.09290.0994-2.72432.574-1.35097.04840.09730.32210.7170.0560.1679-0.1493-0.4969-0.0039-0.26520.00540.02460.00520.21010.10420.20452.671828.449650.7999
44.6804-0.6134-1.72350.83020.32092.0532-0.1302-0.07050.00620.00960.16830.01710.0963-0.042-0.03810.16440.00390.01560.22010.05560.20060.070422.965955.8331
50.67660.4211-0.02510.2041-1.3174.1827-0.0750.09590.09350.03910.08360.1245-0.1704-0.2256-0.00870.1501-0.0012-0.0120.23370.05920.2194-20.471621.415271.8399
68.4191-0.8003-5.12938.70942.365416.7521-0.44571.4745-0.0702-1.4401-0.01570.55060.6925-0.35220.46140.3446-0.0798-0.16980.33260.04710.2498-26.809514.285672.6663
71.9096-0.07770.70811.4154-1.0893.22210.07710.14940.09310.0144-0.1485-0.032-0.20160.24770.07140.1175-0.00680.01340.18240.03490.1384-13.790318.618784.7103
839.3175-24.37665.272241.7387-1.666830.60260.5788-0.69071.2083-0.6628-0.18821.2954-1.5431-1.1873-0.39060.26740.07650.01460.2947-0.04490.2964-24.633635.607673.2511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA246 - 2558 - 17
2X-RAY DIFFRACTION2AA256 - 30718 - 69
3X-RAY DIFFRACTION3AA308 - 34170 - 103
4X-RAY DIFFRACTION4AA342 - 422104 - 184
5X-RAY DIFFRACTION5BB248 - 30710 - 69
6X-RAY DIFFRACTION6BB308 - 32270 - 84
7X-RAY DIFFRACTION7BB323 - 41185 - 173
8X-RAY DIFFRACTION8BB412 - 419174 - 181

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