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- PDB-2yoz: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -

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Basic information

Entry
Database: PDB / ID: 2yoz
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, crystallized with 2'-AMPS
Components2,3-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE
KeywordsHYDROLASE / MYELIN / NERVOUS SYSTEM
Function / homology
Function and homology information


cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath abaxonal region / myelin sheath adaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath abaxonal region / myelin sheath adaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / axonogenesis / adult locomotory behavior / cell projection / response to toxic substance / melanosome / myelin sheath / mitochondrial inner membrane / microtubule / mitochondrial outer membrane / response to lipopolysaccharide / perinuclear region of cytoplasm / extracellular space / RNA binding / membrane / cytoplasm
Similarity search - Function
: / 2',3'-cyclic nucleotide 3'-phosphodiesterase fold / 2',3'-cyclic nucleotide 3'-phosphodiesterase superfamily / Cyclic nucleotide phosphodiesterase / 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase) / Cyclic phosphodiesterase / AAA domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2'-O-(sulfidophosphinato)adenosine / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMyllykoski, M. / Raasakka, A. / Lehtimaki, M. / Han, H. / Kursula, P.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystallographic Analysis of the Reaction Cycle of 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family
Authors: Myllykoski, M. / Raasakka, A. / Lehtimaki, M. / Han, H. / Kursula, I. / Kursula, P.
History
DepositionOct 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 2.0May 15, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / database_PDB_rev ...atom_site / database_PDB_rev / database_PDB_rev_record / diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_auth_atom_name / _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,3-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2599
Polymers24,2941
Non-polymers9658
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.400, 47.880, 51.150
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2,3-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE / CNP / CNPASE


Mass: 24293.928 Da / Num. of mol.: 1 / Fragment: C-TERMINAL CATALYTIC DOMAIN, RESIDUES 159-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PTH 27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase

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Non-polymers , 6 types, 105 molecules

#2: Chemical ChemComp-OVE / 2'-O-(sulfidophosphinato)adenosine / ADENOSINE-2'-MONOPHOSPHOROTHIOATE


Mass: 363.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL GLYCINE REMAINS FROM TEV-CLEAVAGE OF EXPRESSION TAG. RESIDUE NUMBERING IS ACCORDING TO ...N-TERMINAL GLYCINE REMAINS FROM TEV-CLEAVAGE OF EXPRESSION TAG. RESIDUE NUMBERING IS ACCORDING TO CNPASE ISOFORM 1 ( P16330-2).

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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: 1.9 Å3/Da / Density % sol: 35.1 % / Description: NONE
Crystal growTemperature: 277 K / pH: 4
Details: 250 UM PROTEIN AND 10 MM 2, 3(SP)-CYCLIC-AMPS MIXED IN 0.5 PLUS 0.5 DROPS WITH 30% PEG4000 AND 50 MM ACETATE (1:1 MIX OF PH 3 AND PH 5) IN 4C TEMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Apr 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.1→19.1 Å / Num. obs: 10896 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 28.21 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMI

2xmi


Resolution: 2.1→16.999 Å / SU ML: 0.27 / σ(F): 2 / Phase error: 24.59 / Stereochemistry target values: ML
Details: HYDROGENS WERE INCLUDED IN RIDING POSITION. RESIDUES 158-160 AND 206-212 WERE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2222 543 5 %
Rwork0.1748 --
obs0.1773 10872 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→16.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 60 97 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041737
X-RAY DIFFRACTIONf_angle_d0.8172331
X-RAY DIFFRACTIONf_dihedral_angle_d14.293639
X-RAY DIFFRACTIONf_chiral_restr0.046248
X-RAY DIFFRACTIONf_plane_restr0.003293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.31080.30671340.2212549X-RAY DIFFRACTION99
2.3108-2.64410.26881360.20922585X-RAY DIFFRACTION100
2.6441-3.32720.26381360.17122583X-RAY DIFFRACTION100
3.3272-16.99910.17091370.15482612X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.27920.64932.15261.2273-0.5926.28140.0605-0.4499-0.18170.27750.0524-0.60720.3890.5683-0.12240.28410.0265-0.11140.2251-0.02480.256443.609313.489580.2491
24.60844.9383.82466.30724.18393.6887-0.045-0.23460.2291-0.7098-0.1901-0.0369-0.4956-0.28740.28260.23140.0146-0.00720.29760.00340.274422.77869.227964.4478
31.5315-0.37880.64115.19395.0396.039-0.2235-0.1395-0.26780.8608-0.0970.76110.951-0.65080.18530.2939-0.05490.0170.35680.03580.280521.1044-8.372757.4161
41.65661.35090.69564.66311.23822.5618-0.2441-0.1775-0.19090.32870.0568-0.15450.1609-0.09760.09140.21020.0340.04810.1904-0.00760.186340.92037.559375.7989
51.59840.98130.61762.96051.60642.9639-0.07120.1239-0.077-0.22610.1455-0.3135-0.26010.357-0.11860.2108-0.03090.03970.2440.00550.194743.468411.837564.8976
65.610.0342-2.97136.9101-1.25725.4789-0.24040.0008-0.2148-0.1338-0.0324-0.45250.53880.20880.30410.1531-0.0081-0.02030.20790.01270.200337.5669-0.141463.9483
71.04070.04560.32882.85821.00212.8814-0.12590.15720.0828-0.62390.20190.1202-0.34370.0478-0.07610.20380.02310.02650.29270.03440.161631.45747.180456.8875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 161 THROUGH 174 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 175 THROUGH 194 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 195 THROUGH 220 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 221 THROUGH 248 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 249 THROUGH 308 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 309 THROUGH 335 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 336 THROUGH 378 )

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