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- PDB-7pac: The crystal structure of PDE6D in the apo state -

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Basic information

Entry
Database: PDB / ID: 7pac
TitleThe crystal structure of PDE6D in the apo state
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsPROTEIN BINDING / inhibitor / complex
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cilium / intracellular membrane-bounded organelle ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cilium / intracellular membrane-bounded organelle / cytoplasm / cytosol
Similarity search - Function
Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Immunoglobulin E-set
Similarity search - Domain/homology
NICKEL (II) ION / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBeaumont, E. / Williams, D.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA202756
CitationJournal: Blood Cancer J / Year: 2022
Title: Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects.
Authors: Canovas Nunes, S. / De Vita, S. / Anighoro, A. / Autelitano, F. / Beaumont, E. / Klingbeil, P. / McGuinness, M. / Duvert, B. / Harris, C. / Yang, L. / Pokharel, S.P. / Chen, C.W. / Ermann, M. ...Authors: Canovas Nunes, S. / De Vita, S. / Anighoro, A. / Autelitano, F. / Beaumont, E. / Klingbeil, P. / McGuinness, M. / Duvert, B. / Harris, C. / Yang, L. / Pokharel, S.P. / Chen, C.W. / Ermann, M. / Williams, D.A. / Xu, H.
History
DepositionJul 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6503
Polymers19,3531
Non-polymers2972
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint0 kcal/mol
Surface area8330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.250, 39.180, 44.680
Angle α, β, γ (deg.)90.000, 105.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19352.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: O43924
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M Hepes pH7.4, 20 mM MgCl2, 20 mM NiCl2, 20% PEG3350
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.05→42.97 Å / Num. obs: 9410 / % possible obs: 98.8 % / Redundancy: 3 % / CC1/2: 0.961 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.105 / Rrim(I) all: 0.15 / Net I/σ(I): 5.7
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2 / Num. unique obs: 2165 / CC1/2: 0.556 / Rrim(I) all: 0.735 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NAL

5nal


Resolution: 2.05→42.97 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.305 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 470 5.1 %RANDOM
Rwork0.1855 ---
obs0.1879 8804 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.83 Å2 / Biso mean: 24.831 Å2 / Biso min: 13.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-2.08 Å2
2---0.04 Å2-0 Å2
3---0.93 Å2
Refinement stepCycle: final / Resolution: 2.05→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 16 102 1336
Biso mean--40.66 29.86 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131279
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171203
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6591728
X-RAY DIFFRACTIONr_angle_other_deg1.2421.5972792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0535152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68121.94472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6415235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8661510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 38 -
Rwork0.235 631 -
all-669 -
obs--97.81 %

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