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

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Basic information

Entry
Database: PDB / ID: 2yph
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H230S, crystallized with 2',3-(RP)- cyclic-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 / oligodendrocyte differentiation / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / extracellular space ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / oligodendrocyte differentiation / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / 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 / Chem-QQY / 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 30, 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 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 2.1May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Dec 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)24,6834
Polymers24,2431
Non-polymers4403
Water1,42379
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.630, 47.530, 107.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24242.857 Da / Num. of mol.: 1 / Fragment: C-TERMINAL CATALYTIC DOMAIN, RESIDUES 159-278 / Mutation: YES
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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-QQY / [(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanylidene-2-sulfanyl-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol


Mass: 345.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O5PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsADENOSINE-2',3'-CYCLOPHOSPHOROTHIOATE (QQY): RP-ISOMER
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). HISTIDINE 230 IS MUTATED TO SERINE.

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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: 2.1 Å3/Da / Density % sol: 41.4 % / Description: NONE
Crystal growTemperature: 277 K / pH: 4
Details: 250 UM PROTEIN AND 10 MM 23-(RP)-CYCLIC AMPS WAS MIXED IN 0.5 PLUS 0.5 UL DROPS WITH 30% PEG4000 AND 50 MM ACETATE (2:1 PH 3 AND 5) IN 4C TEMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2012
Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M)
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.1→39 Å / Num. obs: 12336 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / % possible all: 92.1

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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→26.887 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 33.69 / Stereochemistry target values: ML
Details: HYDROGENS WERE INCLUDED IN RIDING POSITION. RESIDUES 158-162 AND 209-212 WERE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2888 614 5 %
Rwork0.2301 --
obs0.2329 12327 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 27 79 1748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021741
X-RAY DIFFRACTIONf_angle_d0.5022358
X-RAY DIFFRACTIONf_dihedral_angle_d11.441648
X-RAY DIFFRACTIONf_chiral_restr0.032256
X-RAY DIFFRACTIONf_plane_restr0.002298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.31110.3891420.36252712X-RAY DIFFRACTION92
2.3111-2.64520.31631530.28312904X-RAY DIFFRACTION97
2.6452-3.33170.30381560.23972965X-RAY DIFFRACTION99
3.3317-26.88970.25211630.18493132X-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)
13.4131-1.20791.46134.3342-0.6853.80910.0184-0.00170.02090.331-0.05020.0158-0.05840.24060.04590.2819-0.05560.08580.321-0.01510.2824-1.66617.1914-18.4362
25.52940.62761.48243.5499-0.90087.16760.0471-0.2607-0.73290.2014-0.23830.82150.1354-0.73970.20810.52720.03570.28050.5376-0.00570.7249-16.46619.5424-13.5592
32.1328-1.21010.85734.2129-1.56023.3058-0.0969-0.3646-0.08881.03790.07410.0466-0.12190.06660.03550.5088-0.01470.07350.3976-0.01560.3695-1.54835.0435-9.9437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 163 THROUGH 280 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 281 THROUGH 308 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 309 THROUGH 378 )

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