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- PDB-4z2b: The structure of human PDE12 residues 161-609 in complex with GSK... -

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Basic information

Entry
Database: PDB / ID: 4z2b
TitleThe structure of human PDE12 residues 161-609 in complex with GSK3036342A
Components2',5'-phosphodiesterase 12
KeywordsHydrolase/Hydrolase Inhibitor / PDE12 2'-5'A EEP nuclease Inhibitor complex / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


oligoribonucleotidase activity / mitochondrial mRNA catabolic process / regulation of mitochondrial mRNA stability / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / cellular response to interferon-alpha / nucleic acid metabolic process / OAS antiviral response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / cellular response to dsRNA ...oligoribonucleotidase activity / mitochondrial mRNA catabolic process / regulation of mitochondrial mRNA stability / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / cellular response to interferon-alpha / nucleic acid metabolic process / OAS antiviral response / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / cellular response to dsRNA / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / exonuclease activity / antiviral innate immune response / positive regulation of viral genome replication / mRNA processing / cellular response to type II interferon / 3'-5'-RNA exonuclease activity / defense response to virus / mitochondrial matrix / mitochondrion / metal ion binding / cytosol
Similarity search - Function
: / 2',5'-phosphodiesterase 12-like, N-terminal domain / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
Chem-4LC / 2',5'-phosphodiesterase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsNolte, R.T. / Wisely, B. / Wang, L. / Wood, E.R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors.
Authors: Wood, E.R. / Bledsoe, R. / Chai, J. / Daka, P. / Deng, H. / Ding, Y. / Harris-Gurley, S. / Kryn, L.H. / Nartey, E. / Nichols, J. / Nolte, R.T. / Prabhu, N. / Rise, C. / Sheahan, T. / ...Authors: Wood, E.R. / Bledsoe, R. / Chai, J. / Daka, P. / Deng, H. / Ding, Y. / Harris-Gurley, S. / Kryn, L.H. / Nartey, E. / Nichols, J. / Nolte, R.T. / Prabhu, N. / Rise, C. / Sheahan, T. / Shotwell, J.B. / Smith, D. / Tai, V. / Taylor, J.D. / Tomberlin, G. / Wang, L. / Wisely, B. / You, S. / Xia, B. / Dickson, H.
History
DepositionMar 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2',5'-phosphodiesterase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9967
Polymers51,1381
Non-polymers8586
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.309, 66.532, 124.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2',5'-phosphodiesterase 12 / 2-PDE / Mitochondrial deadenylase


Mass: 51137.672 Da / Num. of mol.: 1 / Fragment: UNP residues 155-609
Source method: isolated from a genetically manipulated source
Details: Tev cloning tag on N-terminus / Source: (gene. exp.) Homo sapiens (human) / Gene: PDE12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: Q6L8Q7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, poly(A)-specific ribonuclease

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Non-polymers , 6 types, 468 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-4LC / 3-(6-{[(2S,3S)-3-(hydroxymethyl)-2-phenylmorpholin-4-yl]carbonyl}-1-methyl-1H-benzimidazol-2-yl)-1H-indole-6-carbonitrile


Mass: 491.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H25N5O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris Ph 8.5 15% Peg20000 25% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 12, 2012
RadiationMonochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 4.8 % / Number: 194359 / Rmerge(I) obs: 0.054 / Χ2: 0.94 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 40745 / % possible obs: 91.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.885010.0531.6996.3
3.884.8810.0350.965.4
3.393.8810.0360.8814.3
3.083.3910.0380.7715.8
2.863.0810.0440.7396.1
2.692.8610.050.786.2
2.552.6910.0580.816.1
2.442.5510.0640.7756
2.352.4410.0710.8175.9
2.272.3510.1020.9775.5
2.22.2710.1161.5614.4
2.132.210.1030.8564.5
2.082.1310.0990.834.2
2.032.0810.1120.8534
1.982.0310.1260.8143.7
1.941.9810.1620.783.4
1.91.9410.1631.1093.2
1.861.910.3130.8363
1.831.8610.2620.722.5
1.81.8310.2660.7262.1
ReflectionResolution: 1.8→50 Å / Num. obs: 40745 / % possible obs: 91.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.62 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.10.26614370.9040.1950.3320.72666.1
1.83-1.862.50.26216700.9120.180.320.7276.3
1.86-1.930.31318000.9410.20.3740.83682.7
1.9-1.943.20.16318860.9410.0990.1911.10986.4
1.94-1.983.40.16219720.970.0950.1890.7890.3
1.98-2.033.70.12620490.9810.0710.1460.81493.5
2.03-2.0840.11221180.9790.0620.1290.85395.7
2.08-2.134.20.09920790.9870.0520.1120.8397.2
2.13-2.24.50.10321370.9890.0520.1160.85697.4
2.2-2.274.40.11621410.9770.060.1321.56197
2.27-2.355.50.10222030.9930.0470.1130.97799.1
2.35-2.445.90.07121590.9950.0320.0780.81798.9
2.44-2.5560.06421990.9960.0280.070.77599.1
2.55-2.696.10.05821900.9970.0250.0630.8199.3
2.69-2.866.20.0521980.9970.0220.0550.7899.5
2.86-3.086.10.04422200.9980.0190.0480.73999.5
3.082-3.395.80.03822340.9980.0180.0420.77199.7
3.392-3.884.30.03613930.9980.0180.040.88162
3.883-4.885.40.03522800.9980.0170.0390.9699.2
4.882-506.30.05323800.9970.0230.0581.69998.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.61 Å27.3 Å
Translation6.61 Å27.3 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.1phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NG0

3ng0


Resolution: 1.8→27.3 Å / Cor.coef. Fo:Fc: 0.9524 / Cor.coef. Fo:Fc free: 0.9254 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.153 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1255 3.15 %RANDOM
Rwork0.1815 ---
obs0.1827 39837 89.99 %-
Displacement parametersBiso mean: 21.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.4148 Å20 Å20 Å2
2--0.1225 Å20 Å2
3---0.2923 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 59 462 4100
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013743HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.985104HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1673SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes548HARMONIC5
X-RAY DIFFRACTIONt_it3743HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.99
X-RAY DIFFRACTIONt_other_torsion2.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion473SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4786SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2505 48 2.82 %
Rwork0.2227 1652 -
all0.2234 1700 -
obs--89.99 %

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