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

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Basic information

Entry
Database: PDB / ID: 2ypc
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H309S, crystallized with 2',3-(SP)-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 / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / pseudopodium / oligodendrocyte differentiation / 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 / pseudopodium / oligodendrocyte differentiation / microvillus / forebrain development / axonogenesis / adult locomotory behavior / cell projection / response to toxic substance / melanosome / myelin sheath / mitochondrial outer membrane / response to lipopolysaccharide / mitochondrial inner membrane / perinuclear region of cytoplasm / RNA binding / extracellular space / 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
Chem-QQX / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.894 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 1.3Jul 15, 2015Group: Data collection
Revision 1.4Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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 / _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)24,5882
Polymers24,2431
Non-polymers3451
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.280, 47.490, 53.760
Angle α, β, γ (deg.)90.00, 94.89, 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, RESIDUES 159-378 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Chemical ChemComp-QQX / [(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanyl-2-sulfanylidene-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol / ADENOSINE-2',3'-CYCLOPHOSPHOROTHIOATE


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


Mass: 18.015 Da / Num. of mol.: 204 / 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 2 ( 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: 40.6 % / Description: NONE
Crystal growpH: 4
Details: 250 UM PROTEIN AND 10 MM 23(SP)-CYCLIC-AMPS MIXED IN 0.5 PLUS 0.5 UL DROPS WITH 25% PEG6000 AND 50 MM ACETATE (PH3:PH5 2:1) IN RT, pH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.22343
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22343 Å / Relative weight: 1
ReflectionResolution: 1.89→40.1 Å / Num. obs: 15833 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.83 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.4
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.3 / % possible all: 82.4

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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: 1.894→40.133 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 21.68 / Stereochemistry target values: ML
Details: HYDROGENS WERE INCLUDED IN RIDING POSITION. RESIDUES 158-162 AND 336-337 WERE EXCLUDED DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2128 792 5 %
Rwork0.1645 --
obs0.167 15832 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.15 Å2
Refinement stepCycle: LAST / Resolution: 1.894→40.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 22 204 1893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081756
X-RAY DIFFRACTIONf_angle_d1.032376
X-RAY DIFFRACTIONf_dihedral_angle_d13.297655
X-RAY DIFFRACTIONf_chiral_restr0.061257
X-RAY DIFFRACTIONf_plane_restr0.005301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8941-2.01280.22271210.18532307X-RAY DIFFRACTION90
2.0128-2.16820.24861320.16152510X-RAY DIFFRACTION99
2.1682-2.38640.21651330.15632524X-RAY DIFFRACTION99
2.3864-2.73160.21161340.16982542X-RAY DIFFRACTION99
2.7316-3.44120.21311340.1652554X-RAY DIFFRACTION99
3.4412-40.14210.20091380.16192603X-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)
12.521-0.8686-0.34714.3478-2.14633.0298-0.04-0.34330.08570.03480.0906-0.34320.16650.1720.02920.15740.05690.00170.1801-0.02880.17997.90336.077228.3417
22.26231.29840.96765.44041.90943.8124-0.09210.06350.43540.16280.08240.5375-0.023-0.44440.03290.14440.01960.00380.24290.04180.2371-11.6772.425714.4725
32.8583-0.40350.58582.6094-0.59234.6935-0.20190.3922-0.7848-0.50340.32430.34741.122-0.7374-0.17940.4676-0.1093-0.02150.3803-0.02370.3679-12.2184-18.22387.7407
40.5860.8110.23751.2921-0.03740.7334-0.012-0.0280.10060.07530.0110.1220.2089-0.1024-0.00780.18690.01330.04460.17680.0080.18240.6292-2.671524.0706
51.18150.20750.35631.7484-0.1521.5856-0.09250.080.1194-0.00380.0565-0.2046-0.21210.19980.02350.1443-0.02630.02080.1536-0.00570.14698.1817.03617.3765
61.61.2765-0.34343.46341.26741.0465-0.1979-0.2965-1.05820.4612-0.0873-1.02320.95160.9683-0.01250.4390.18120.0310.47480.07170.530716.7966-2.534317.071
71.33240.8127-0.43572.5217-0.13041.9257-0.1456-0.0056-0.3023-0.11530.0639-0.54420.23510.25930.06510.19280.01330.02350.1659-0.00480.22965.0899-5.739314.4157
80.76840.13551.12710.81920.4552.0377-0.19280.22970.0981-0.34940.29970.01070.1231-0.083-0.11550.4249-0.0971-0.03350.30630.00750.1253-3.8192-4.5499-1.499
91.24770.61660.68411.425-0.06061.8874-0.15490.22110.131-0.18730.12490.1342-0.1234-0.08970.04120.1491-0.00470.03430.18760.02270.1689-0.81944.049513.179
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 288 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 289 THROUGH 299 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 300 THROUGH 333 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 334 THROUGH 355 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 356 THROUGH 378 )

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