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- PDB-4zkf: Crystal structure of human phosphodiesterase 12 -

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Basic information

Entry
Database: PDB / ID: 4zkf
TitleCrystal structure of human phosphodiesterase 12
Components2',5'-phosphodiesterase 12
KeywordsHYDROLASE / Diesterase
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 / Resolution: 1.82 Å
AuthorsKim, S.Y. / Kohno, T. / Mori, T. / Kitano, K. / Hakoshima, T.
CitationJournal: To Be Published
Title: Crystal structure of human phosphodiesterase
Authors: Kim, S.Y. / Kohno, T. / Mori, T. / Kitano, K. / Hakoshima, T.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Structure summary
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _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)51,9463
Polymers51,8981
Non-polymers492
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-17 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.817, 99.840, 104.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 51897.535 Da / Num. of mol.: 1 / Fragment: UNP residues 154-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE12 / Production host: Escherichia coli (E. coli)
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 43956 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.095 / Χ2: 1.671 / Net I/av σ(I): 24.625 / Net I/σ(I): 9.9 / Num. measured all: 240887
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.82-1.894.60.50942951.2599.2
1.89-1.965.40.40743131.28100
1.96-2.055.60.29743451.331100
2.05-2.165.60.21843411.397100
2.16-2.295.70.16943821.433100
2.29-2.475.70.1343301.438100
2.47-2.725.70.09844121.455100
2.72-3.115.70.07744131.829100
3.11-3.925.30.06544593.046100
3.92-505.40.04446662.18299.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
PHASERdata reduction
PHASERphasing
RefinementResolution: 1.82→33.755 Å / FOM work R set: 0.8872 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 2237 5.1 %
Rwork0.1657 41652 -
obs0.167 43889 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.41 Å2 / Biso mean: 22.36 Å2 / Biso min: 6.45 Å2
Refinement stepCycle: final / Resolution: 1.82→33.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 2 463 4121
Biso mean--24.12 30.8 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073757
X-RAY DIFFRACTIONf_angle_d1.1285114
X-RAY DIFFRACTIONf_chiral_restr0.047561
X-RAY DIFFRACTIONf_plane_restr0.006663
X-RAY DIFFRACTIONf_dihedral_angle_d13.4521370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8192-1.85880.24791380.24042515265398
1.8588-1.9020.27881680.21625472715100
1.902-1.94960.21551480.191825262674100
1.9496-2.00230.21611470.176825812728100
2.0023-2.06120.18591260.166625732699100
2.0612-2.12770.22991350.169925842719100
2.1277-2.20370.20991370.170325862723100
2.2037-2.29190.23141260.167126132739100
2.2919-2.39620.19761220.166425892711100
2.3962-2.52250.19051590.169125642723100
2.5225-2.68050.19541220.173926412763100
2.6805-2.88740.17081440.167325922736100
2.8874-3.17770.20561400.162426182758100
3.1777-3.63710.16931460.150626372783100
3.6371-4.58050.14251330.135926982831100
4.5805-33.76080.17131460.170627882934100

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