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- PDB-2yp0: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -

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Basic information

Entry
Database: PDB / ID: 2yp0
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
ACETIC ACID / 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: 2.3 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 2.0Jun 14, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_struct_sheet_hbond ...atom_site / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
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.auth_seq_id / _atom_site.label_atom_id / _atom_site.type_symbol / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet.number_strands / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)25,4116
Polymers24,2941
Non-polymers1,1175
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.830, 47.740, 50.930
Angle α, β, γ (deg.)90.00, 97.87, 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) / 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 , 5 types, 81 molecules

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


Mass: 363.287 Da / Num. of mol.: 2 / 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-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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 MOUSE 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: 36.6 % / Description: NONE
Crystal growpH: 4
Details: 250 UM PROTEIN AND 10 MM 2, 3(RP)-CYCLIC-AMPS MIXED WITH 0.5 PLUS 0.5 DROPS WITH 30% PEG4000 AND 50 MM ACETATE (MIX OF PH 3 AND PH 5 IN 2:1 RATIO) AT RT

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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: 2.3→19.4 Å / Num. obs: 8391 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 27.95 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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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: 2.3→19.29 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 30.09 / Stereochemistry target values: ML
Details: HYDROGENS WERE INCLUDED IN RIDING POSITIONS. RESIDUES 158-162 AND 208-213 WERE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2694 418 5 %
Rwork0.2112 --
obs0.2142 8367 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.93 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 72 76 1781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031743
X-RAY DIFFRACTIONf_angle_d0.6572348
X-RAY DIFFRACTIONf_dihedral_angle_d15.444635
X-RAY DIFFRACTIONf_chiral_restr0.038254
X-RAY DIFFRACTIONf_plane_restr0.003288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.63250.32671400.23762663X-RAY DIFFRACTION100
2.6325-3.3140.29051410.23172688X-RAY DIFFRACTION100
3.314-19.29080.24031370.1912598X-RAY DIFFRACTION95
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)
11.7315-1.1154-0.70381.45330.10860.63220.0018-0.2775-0.40960.2630.0911-0.21250.11920.17-0.13440.12820.029-0.08490.24210.07320.340539.368514.546877.262
22.8624.56743.45988.13396.06226.5619-0.3255-0.10740.48050.35560.14130.9461-0.0933-0.07880.2520.21430.0755-0.04230.28170.06190.291920.298910.270863.3263
37.869-2.7004-3.58265.1402-0.5933.77890.15590.4103-0.56550.323-0.243-0.18250.534-0.3173-0.09140.3227-0.1357-0.04580.21220.02740.401820.855-8.577955.6467
42.12731.58271.70851.29590.93892.27310.1112-0.15230.0215-0.0919-0.10610.00320.1812-0.1971-0.01130.14370.0147-0.05130.18440.03690.171632.94335.720473.145
51.0089-0.2911.63234.04441.53584.021-0.28320.21640.1542-0.13230.2139-0.5414-0.61060.49650.09590.2163-0.06620.03380.32140.03330.29741.813418.194669.4652
64.78673.4861.09435.08880.24450.7876-0.1230.3504-0.57730.07790.2126-0.55260.0560.3122-0.0620.2247-0.00510.00040.2659-0.0140.215841.63049.335363.5534
74.68551.2309-2.53313.803-1.783.9941-0.2428-0.1176-0.5362-0.0384-0.2014-0.62230.35310.35840.41850.1990.0227-0.050.18590.00130.303836.85512.234163.4688
82.7405-1.74760.52814.71160.47761.42580.55640.237-0.1756-0.8161-0.1325-0.12070.38920.2645-0.32330.46190.0033-0.05370.1801-0.07820.248429.13082.385548.2762
90.91440.0591.21622.25411.08552.1805-0.0272-0.07070.236-0.2643-0.16160.1517-0.3257-0.0120.23720.1086-0.04540.03680.1567-0.04110.275930.996714.12663.3814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 163 THROUGH 174 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 175 THROUGH 193 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 194 THROUGH 216 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 217 THROUGH 243 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 244 THROUGH 270 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 271 THROUGH 299 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 300 THROUGH 333 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 334 THROUGH 358 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 359 THROUGH 378 )

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