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- PDB-4z0v: The structure of human PDE12 residues 161-609 -

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Basic information

Entry
Database: PDB / ID: 4z0v
TitleThe structure of human PDE12 residues 161-609
Components2',5'-phosphodiesterase 12
KeywordsHYDROLASE / PDE12 2'-5'A EEP nuclease
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
2',5'-phosphodiesterase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 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 26, 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,2348
Polymers49,6571
Non-polymers5777
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.688, 62.554, 65.393
Angle α, β, γ (deg.)90.00, 110.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 49657.113 Da / Num. of mol.: 1 / Fragment: UNP residues 155-609
Source method: isolated from a genetically manipulated source
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M MgCl2 0.1M Tris pH 8.5 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 41250 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.41 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.694
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.843.80.40241160.8630.2420.471.091100
1.84-1.923.80.29540800.930.1760.3441.109100
1.92-23.80.20641190.9620.1240.2411.048100
2-2.113.80.14941120.9780.0890.1741.048100
2.11-2.243.80.11940860.9840.0710.1380.988100
2.24-2.423.80.09241460.990.0550.1080.952100
2.42-2.663.80.07640800.9930.0450.0881.007100
2.66-3.043.80.07341400.9930.0430.0851.151100
3.04-3.833.70.0641490.9940.0360.071.00799.8
3.83-503.70.03542220.9980.0210.040.89199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å43.78 Å
Translation1.8 Å43.78 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.4phasing
PDB_EXTRACT3.15data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NG0

3ng0


Resolution: 1.78→43.78 Å / Cor.coef. Fo:Fc: 0.9543 / Cor.coef. Fo:Fc free: 0.9413 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1291 3.13 %RANDOM
Rwork0.1645 ---
obs0.1657 41211 99.96 %-
Displacement parametersBiso mean: 21.18 Å2
Baniso -1Baniso -2Baniso -3
1-3.9537 Å20 Å2-0.7934 Å2
2---2.0526 Å20 Å2
3----1.9011 Å2
Refine analyzeLuzzati coordinate error obs: 0.172 Å
Refinement stepCycle: LAST / Resolution: 1.78→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 37 360 3850
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013584HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1623SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes531HARMONIC5
X-RAY DIFFRACTIONt_it3584HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.11
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion461SEMIHARMONIC5
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_contact4361SEMIHARMONIC4
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2086 93 3.05 %
Rwork0.202 2959 -
all0.2022 3052 -
obs--99.96 %

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