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

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Basic information

Entry
Database: PDB / ID: 2ype
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H309S, crystallized with 2',3'- cyclic AMP
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 adaxonal region / myelin sheath abaxonal 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 adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / response to lipopolysaccharide / mitochondrial outer membrane / mitochondrial inner membrane / 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
2',3'- cyclic AMP / ACETIC ACID / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 2.0Dec 20, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / pdbx_validate_close_contact
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 / _chem_comp.name / _citation.page_last / _entity.pdbx_description / _entity.pdbx_mutation / _pdbx_validate_close_contact.auth_atom_id_1
Revision 2.1May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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)24,7285
Polymers24,2431
Non-polymers4854
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.800, 47.130, 53.780
Angle α, β, γ (deg.)90.00, 94.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24242.859 Da / Num. of mol.: 1 / Fragment: C-TERMINAL CATALYTIC DOMAIN / Mutation: H309S
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
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACK / 2',3'- cyclic AMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
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 309 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 % / Description: NONE
Crystal growTemperature: 277 K / pH: 4
Details: 250 UM PROTEIN AND 10 MM 23-CYCLIC AMP MIXED IN 0.5 PLUS 0.5 DROPS WITH 50 MM SODIUM ACETATE (1:1, PH3:PH5) AND 23% PEG 4000 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
DetectorDate: Apr 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 16037 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.5 / % possible all: 98.5

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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: 1.9→9.996 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 21.11 / Stereochemistry target values: ML
Details: HYDROGENS WERE ADDED IN RIDING POSITION. RESIDUES 158-161 AND 336-338 WERE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.207 802 5 %
Rwork0.1667 --
obs0.1687 16032 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→9.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 31 263 1964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021771
X-RAY DIFFRACTIONf_angle_d0.692393
X-RAY DIFFRACTIONf_dihedral_angle_d10.879660
X-RAY DIFFRACTIONf_chiral_restr0.041257
X-RAY DIFFRACTIONf_plane_restr0.002303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.01820.32861310.25422501X-RAY DIFFRACTION99
2.0182-2.17260.23651330.20532523X-RAY DIFFRACTION100
2.1726-2.38850.21851330.18362529X-RAY DIFFRACTION100
2.3885-2.7280.24771340.18262533X-RAY DIFFRACTION100
2.728-3.4140.18431340.1522549X-RAY DIFFRACTION100
3.414-9.9960.17131370.13792595X-RAY DIFFRACTION100
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)
11.82840.74750.24092.98891.18611.8715-0.1418-0.15190.2827-0.0780.03190.2118-0.1607-0.23010.17130.14520.03470.01620.18430.02430.16233.843711.720774.3579
27.42021.11640.42873.85330.65762.12660.24130.1092-0.7807-0.3035-0.00590.47621.3859-0.3410.01490.5323-0.0944-0.06530.3393-0.03160.365224.8493-11.058361.6717
31.2760.70840.28242.49560.11551.6241-0.07450.01050.0494-0.00790.0681-0.1067-0.12030.07710.01690.11330.01750.01760.14570.00630.120342.534811.046873.6481
45.30550.95352.14524.7873.65533.18250.15830.0956-0.9280.14970.0401-0.7481.01710.5954-0.15640.40130.07250.02720.5149-0.01580.383554.03044.757370.7422
52.75581.0011-1.23283.1185-0.52523.491-0.04710.0553-0.1929-0.36490.0281-0.32020.06280.25690.0720.168-0.00040.01420.1761-0.0240.199842.0911.542667.7171
60.30330.36290.79532.23690.21522.38570.09710.40590.154-0.5680.1665-0.15810.51750.3873-0.15140.3614-0.0177-0.09450.4664-0.02840.261432.22083.042151.1313
71.67140.61921.33973.04981.54573.4219-0.12840.18240.0305-0.40770.08580.0837-0.1629-0.01760.02050.0873-0.03120.06780.16340.01920.120335.40079.250664.2504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 162 THROUGH 194 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 195 THROUGH 216 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 217 THROUGH 288 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 289 THROUGH 299 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 300 THROUGH 334 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 335 THROUGH 348 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 349 THROUGH 378 )

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