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- PDB-4wbl: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -

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Basic information

Entry
Database: PDB / ID: 4wbl
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation F235A
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
2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsMyllykoski, M. / Raasakka, A. / Kursula, P.
CitationJournal: Sci Rep / Year: 2015
Title: Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase.
Authors: Raasakka, A. / Myllykoski, M. / Laulumaa, S. / Lehtimaki, M. / Hartlein, M. / Moulin, M. / Kursula, I. / Kursula, P.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)24,3814
Polymers24,2181
Non-polymers1633
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-26 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.220, 47.770, 54.090
Angle α, β, γ (deg.)90.000, 94.730, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein 2',3'-cyclic-nucleotide 3'-phosphodiesterase / CNPase


Mass: 24217.830 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 179-398 / Mutation: F235A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnp, Cnp1 / Plasmid: pTH27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-acetate, PEG 4000/6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.223 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.223 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 7167 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 30.57 Å2 / Rmerge F obs: 0.228 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.178 / Χ2: 0.857 / Net I/σ(I): 6.85 / Num. measured all: 25813
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.573.60.930.7691.8518555135150.904100
2.57-2.640.8540.6762.0318375055040.79399.8
2.64-2.710.7380.5752.3718925215200.67699.8
2.71-2.80.6170.4642.9317514754760.545100
2.8-2.890.5170.4113.2717594814790.48299.6
2.89-2.990.4040.3074.2416474454460.359100
2.99-3.10.3650.2844.6616324484470.33399.8
3.1-3.230.2550.2056.1415414214210.24100
3.23-3.370.1620.1587.315164194180.18699.8
3.37-3.540.1250.1288.5913453653640.1599.7
3.54-3.730.1240.1189.2813673823810.1499.7
3.73-3.950.090.09810.6812683513500.11599.7
3.95-4.230.0750.08111.612073353330.09599.4
4.23-4.570.0790.08212.4710753053040.09699.7
4.57-50.0780.08812.6210632952950.103100
5-5.590.0790.08111.78802542530.09599.6
5.59-6.460.0890.09411.648012342320.11199.1
6.46-7.910.0720.07811.946552012010.094100
7.91-11.190.0470.06715.054691491440.0896.6
11.190.0520.06415.3125393840.07990.3

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xmi

2xmi


Resolution: 2.501→27.437 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 359 5.01 %
Rwork0.195 6808 -
obs0.1983 7167 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.34 Å2 / Biso mean: 46.5159 Å2 / Biso min: 6.25 Å2
Refinement stepCycle: final / Resolution: 2.501→27.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 15 68 1715
Biso mean--61.14 28.84 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021706
X-RAY DIFFRACTIONf_angle_d0.6062298
X-RAY DIFFRACTIONf_chiral_restr0.024248
X-RAY DIFFRACTIONf_plane_restr0.003292
X-RAY DIFFRACTIONf_dihedral_angle_d12.198640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5012-2.86280.3651180.270722362354100
2.8628-3.60560.29731200.20722792399100
3.6056-27.43860.21141210.16022293241499
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)
14.17651.39521.6373.64361.46672.2772-0.1052-0.25270.4-0.0220.00010.3423-0.0589-0.43530.08940.30020.01720.07840.33740.04460.204475.375411.386819.234
23.23681.6881-1.16681.68461.27477.1401-0.23520.4218-0.6726-0.2679-0.13240.27521.4851-0.76680.34580.6843-0.2227-0.01210.54490.02980.467268.6825-8.36599.0176
31.66720.75960.35842.13230.94933.6541-0.14120.01330.0172-0.00530.0355-0.1603-0.00580.24070.11160.26420.05360.05720.23110.01960.302287.328112.501320.2301
44.8203-4.4405-3.87354.1933.65883.2016-0.23110.1796-0.89550.9367-0.52240.11921.29090.56190.55310.71550.05580.04950.68980.05720.466197.20465.104516.6778
52.44132.19540.5624.2196-2.13814.1653-0.0352-0.3093-0.40690.036-0.0718-0.66110.23090.63810.12390.27750.05580.06030.27450.01330.381285.15533.316315.9071
61.64740.87741.78972.5550.91542.6244-0.12780.2651-0.0758-0.54340.1133-0.04140.06080.03850.00920.4225-0.03410.14690.34990.03350.376780.08546.37658.4037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 194 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 220 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 288 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 299 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 300 through 319 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 378 )A0

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