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- PDB-5e8f: Structure of Fully modified geranylgeranylated PDE6C Peptide in c... -

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Basic information

Entry
Database: PDB / ID: 5e8f
TitleStructure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D
Components
  • Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsHYDROLASE / Prenyl binding protein / Immunoglobulin-like beta sandwitch fold / geranylgeranyl
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / retinal cone cell development / 3',5'-cyclic-GMP phosphodiesterase / GTPase inhibitor activity / phototransduction, visible light / response to stimulus / 3',5'-cyclic-GMP phosphodiesterase activity / cGMP binding / 3',5'-cyclic-nucleotide phosphodiesterase activity / visual perception ...ARL13B-mediated ciliary trafficking of INPP5E / retinal cone cell development / 3',5'-cyclic-GMP phosphodiesterase / GTPase inhibitor activity / phototransduction, visible light / response to stimulus / 3',5'-cyclic-GMP phosphodiesterase activity / cGMP binding / 3',5'-cyclic-nucleotide phosphodiesterase activity / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / 3'5'-cyclic nucleotide phosphodiesterase / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site ...GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / 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 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
GERAN-8-YL GERAN / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFansa, E.K. / O'Reilly, N.J. / Ismail, S.A. / Wittinghofer, A.
CitationJournal: Embo Rep. / Year: 2015
Title: The N- and C-terminal ends of RPGR can bind to PDE6 delta.
Authors: Fansa, E.K. / O'Reilly, N.J. / Ismail, S. / Wittinghofer, A.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
C: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
D: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
E: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3326
Polymers35,7834
Non-polymers5492
Water1,946108
1
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
D: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1663
Polymers17,8922
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
E: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1663
Polymers17,8922
Non-polymers2741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.710, 81.430, 118.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GMP-PDE delta / Protein p17


Mass: 17309.793 Da / Num. of mol.: 2 / Fragment: UNP residues 2-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli (E. coli)
References: UniProt: O43924, 3',5'-cyclic-GMP phosphodiesterase
#2: Protein/peptide Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' / cGMP phosphodiesterase 6C


Mass: 581.726 Da / Num. of mol.: 2 / Fragment: UNP residues 851-855
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6C, PDEA2 / Production host: Escherichia coli (E. coli)
References: UniProt: P51160, 3',5'-cyclic-GMP phosphodiesterase
#3: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H34 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES (pH 7.5), 0.2 M Li2SO4, 25 % PEG4000 and 0.1 M NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.1→29.63 Å / Num. obs: 22232 / % possible obs: 99.6 % / Redundancy: 5.29 % / Rsym value: 0.05 / Net I/σ(I): 23.46
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.35 % / Mean I/σ(I) obs: 10.24 / Rsym value: 0.163 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALE5.7.0032data scaling
MOLREP3.15phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5G

3t5g


Resolution: 2.1→29.63 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.7 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1116 5 %RANDOM
Rwork0.1983 ---
obs0.2012 21194 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.69 Å2 / Biso mean: 34.13 Å2 / Biso min: 17.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.11 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 2.1→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 108 2651
Biso mean---38.55 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022591
X-RAY DIFFRACTIONr_bond_other_d0.0020.022533
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.9673477
X-RAY DIFFRACTIONr_angle_other_deg0.9923.0095831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0224.098122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09515481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0221518
X-RAY DIFFRACTIONr_chiral_restr0.1120.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_mcbond_it2.823.011218
X-RAY DIFFRACTIONr_mcbond_other2.823.0091216
X-RAY DIFFRACTIONr_mcangle_it3.7264.4941512
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 82 -
Rwork0.216 1554 -
all-1636 -
obs--100 %

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