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- PDB-3dba: Crystal structure of the cGMP-bound GAF a domain from the photore... -

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Basic information

Entry
Database: PDB / ID: 3dba
TitleCrystal structure of the cGMP-bound GAF a domain from the photoreceptor phosphodiesterase 6C
ComponentsCone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
KeywordsHYDROLASE / 3' / 5' cGMP / GAF domain / cyclic nucleotide phosphodiesterase / cGMP / Lipoprotein / Membrane / Prenylation / Sensory transduction / Vision
Function / homology
Function and homology information


3',5'-cyclic-GMP phosphodiesterase / 3',5'-cyclic-GMP phosphodiesterase activity / cGMP binding / 3',5'-cyclic-nucleotide phosphodiesterase activity / visual perception / signal transduction / metal ion binding / plasma membrane
Similarity search - Function
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 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
GUANOSINE-3',5'-MONOPHOSPHATE / Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 Å
AuthorsMartinez, S.E. / Heikaus, C.C. / Klevit, R.E. / Beavo, J.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Structure of the GAF A Domain from Phosphodiesterase 6C Reveals Determinants of cGMP Binding, a Conserved Binding Surface, and a Large cGMP-dependent Conformational Change.
Authors: Martinez, S.E. / Heikaus, C.C. / Klevit, R.E. / Beavo, J.A.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 / 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 / _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: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
B: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6039
Polymers41,4522
Non-polymers1,1517
Water1,42379
1
A: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
B: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
hetero molecules

A: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
B: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,20618
Polymers82,9044
Non-polymers2,30214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12270 Å2
ΔGint-43 kcal/mol
Surface area30570 Å2
MethodPISA
2
A: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3475
Polymers20,7261
Non-polymers6214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2554
Polymers20,7261
Non-polymers5293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.598, 67.598, 198.533
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' / cGMP phosphodiesterase 6C


Mass: 20725.941 Da / Num. of mol.: 2 / Fragment: GAF A domain (UNP residues 55-225)
Source method: isolated from a genetically manipulated source
Details: cone cells of retina / Source: (gene. exp.) Gallus gallus (chicken) / Strain: Rhode Island red / Gene: PDE6C / Plasmid: pRUNH / Production host: Escherichia coli (E. coli) / Strain (production host): C41 cells
References: UniProt: P52731, 3',5'-cyclic-GMP phosphodiesterase
#2: Chemical ChemComp-35G / GUANOSINE-3',5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS SEQUENCING OF THE EXPRESSION PLASMID REVEALED AN APPARENT MUTATION R93A, ...ACCORDING TO THE AUTHORS SEQUENCING OF THE EXPRESSION PLASMID REVEALED AN APPARENT MUTATION R93A, WITH REFERENCE TO THE MRNA SEQUENCE IN ENTREZ ENTRY NM_204986. HOWEVER, A CHICKEN GENOMIC CONTIG ENTREZ NW_001471719 SHOWS AN ALA CODON GCC INSTEAD OF THE ARG CODON CGC. NEARLY ALL PDE6 SEQUENCES HAVE AN ALA AT THIS POSITION. IN THE MODEL, THIS ALA IS COMPLETELY BURIED IN A PACKED HYDROPHOBIC ENVIRONMENT. THEREFORE, THE ENTREZ MRNA ENTRY LIKELY HAS A TRANSPOSITION ERROR OF THE FIRST TWO BASES IN THIS CODON.

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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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.5 M ammonium sulfate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 25, 2006
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.57→43.85 Å / Num. all: 17389 / Num. obs: 17389 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 57 Å2 / Rsym value: 0.074 / Net I/σ(I): 51.8
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 1715 / Rsym value: 56.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.57→43.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 28.428 / SU ML: 0.282 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.454 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25705 860 5 %RANDOM
Rwork0.22063 ---
obs0.22245 17159 98.15 %-
all-17389 --
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: 68.876 Å2
Baniso -1Baniso -2Baniso -3
1-7.33 Å23.67 Å20 Å2
2--7.33 Å20 Å2
3----11 Å2
Refinement stepCycle: LAST / Resolution: 2.57→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 76 79 2891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222861
X-RAY DIFFRACTIONr_bond_other_d0.0010.021958
X-RAY DIFFRACTIONr_angle_refined_deg1.2592.0013865
X-RAY DIFFRACTIONr_angle_other_deg0.81334806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16125.079126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93615532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6641514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
X-RAY DIFFRACTIONr_nbd_refined0.2160.2673
X-RAY DIFFRACTIONr_nbd_other0.1810.21948
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21368
X-RAY DIFFRACTIONr_nbtor_other0.0830.21568
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.26
X-RAY DIFFRACTIONr_mcbond_it3.07572218
X-RAY DIFFRACTIONr_mcbond_other0.7687682
X-RAY DIFFRACTIONr_mcangle_it3.907102784
X-RAY DIFFRACTIONr_scbond_it2.75271345
X-RAY DIFFRACTIONr_scangle_it3.623101081
LS refinement shellResolution: 2.572→2.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 61 -
Rwork0.354 1170 -
obs--98.88 %
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)
12.4754-1.1617-1.56582.60781.01918.7551-0.01150.0375-0.03470.17160.0040.3088-0.1444-0.7290.0075-0.1307-0.2421-0.0137-0.41250.0515-0.139914.516638.620515.6737
24.3089-1.47562.40845.7070.21287.83510.53010.8492-0.0519-0.9781-0.2802-0.2951.24360.9836-0.250.35730.0284-0.0558-0.18420.0209-0.124138.824717.188914.8022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA55 - 2252 - 172
2X-RAY DIFFRACTION2BB55 - 2252 - 172

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