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- PDB-4wc9: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -

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Basic information

Entry
Database: PDB / ID: 4wc9
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation F235L
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-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 4, 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

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Assembly

Deposited unit
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)24,2601
Polymers24,2601
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.440, 47.810, 54.170
Angle α, β, γ (deg.)90.000, 94.780, 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: 24259.910 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 179-398 / Mutation: F235L
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) / Variant (production host): rosetta
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-acetate, PEG4000/6000

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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→30 Å / Num. obs: 13840 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 25.69 Å2 / Rmerge F obs: 0.159 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.101 / Χ2: 0.932 / Net I/σ(I): 8.78 / Num. measured all: 44773
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
2-2.052.91.0140.6661.91279410109790.80996.9
2.05-2.110.6930.4782.612924103410040.57997.1
2.11-2.170.5390.3743.2528059829530.45397
2.17-2.240.4340.2973.8328869659480.35998.2
2.24-2.310.3810.2474.4726729018800.29997.7
2.31-2.390.3370.2264.8927849088890.27397.9
2.39-2.480.2810.25.6226758458350.2498.8
2.48-2.580.2330.1616.7227128488420.19399.3
2.58-2.70.2010.1377.6226498067970.16498.9
2.7-2.830.1440.1119.1524907507420.13398.9
2.83-2.980.1120.09610.8624967337260.11499
2.98-3.160.0990.08312.2923276766700.09999.1
3.16-3.380.060.06814.9123226726660.0899.1
3.38-3.650.0510.05916.7220505895860.0799.5
3.65-40.0440.05918.0919675605520.0798.6
4-4.470.0410.05618.8917915115040.06798.6
4.47-5.160.0420.05718.5415424484360.06897.3
5.16-6.320.0420.05618.2113073733670.06698.4
6.32-8.940.040.05218.5510413073010.06298
8.940.0370.0519.445391741630.0693.7

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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→27.526 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 691 5 %
Rwork0.2242 13129 -
obs0.2265 13820 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.31 Å2 / Biso mean: 40.3038 Å2 / Biso min: 14.02 Å2
Refinement stepCycle: final / Resolution: 2→27.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 0 157 1755
Biso mean---34.06 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031665
X-RAY DIFFRACTIONf_angle_d0.682248
X-RAY DIFFRACTIONf_chiral_restr0.026244
X-RAY DIFFRACTIONf_plane_restr0.003287
X-RAY DIFFRACTIONf_dihedral_angle_d12.435620
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.15440.35631340.28912567270197
2.1544-2.37110.30251370.25552600273798
2.3711-2.7140.28281390.25792632277199
2.714-3.41830.26621390.22422649278899
3.4183-27.52840.24321420.19192681282398
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)
10.4380.0353-0.03040.45890.0051.5565-0.04010.02260.0064-0.04830.0379-0.00810.0916-0.113100.18620.0048-0.01170.20420.01780.235740.20258.065619.7031
20.46070.24090.49350.12080.25070.7115-0.01920.0138-0.154-0.00510.0209-0.095-0.06020.1092-00.2316-0.0090.04470.22270.01510.239646.87728.060614.6953
30.74170.5155-0.160.5219-0.38640.5048-0.10780.1372-0.0717-0.20740.1714-0.1204-0.0542-0.137800.3352-0.02550.03250.25430.00820.23740.39216.38458.8209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 259 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 260 through 319 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 378 )A0

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