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

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Basic information

Entry
Database: PDB / ID: 4wde
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation T311A
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 / adult locomotory behavior / axonogenesis / 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) / AAA domain / Cyclic phosphodiesterase / 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 / molecular replacement / Resolution: 2.4 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 8, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 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
B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6203
Polymers48,5282
Non-polymers921
Water2,540141
1
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3562
Polymers24,2641
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)24,2641
Polymers24,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.370, 46.440, 107.460
Angle α, β, γ (deg.)90.000, 93.930, 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: 24263.902 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 179-378 / Mutation: T311A
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-citrate, PEG 4000 / 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 16418 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 29.43 Å2 / Rmerge F obs: 0.985 / Rmerge(I) obs: 0.185 / Rrim(I) all: 0.217 / Χ2: 0.906 / Net I/σ(I): 6.99 / Num. measured all: 59872
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
2.4-2.4630.4510.9371.293304122911011.14589.6
2.46-2.530.5710.8811.63919117211591.04598.9
2.53-2.60.690.8161.934347116711620.95399.6
2.6-2.680.7450.6872.324220113211300.80399.8
2.68-2.770.8080.5832.754007107110660.6899.5
2.77-2.870.8790.4473.393953105510530.52199.8
2.87-2.980.9170.3823.953841102210220.445100
2.98-3.10.9360.2985.0836929859850.348100
3.1-3.240.9540.2455.9134779249230.28699.9
3.24-3.390.9730.1738.2633188908890.20299.9
3.39-3.580.9820.1558.5832838808800.181100
3.58-3.790.9880.11810.5129747957960.139100
3.79-4.060.9880.10112.7528227657630.11999.7
4.06-4.380.9930.0815.0326207127100.09499.7
4.38-4.80.9930.07815.9324726726690.09199.6
4.8-5.370.9940.08513.9822246056040.09999.8
5.37-6.20.9910.09412.5619185255230.1199.6
6.2-7.590.9880.10611.3716224484460.12499.6
7.59-10.730.9970.04720.1312843693690.055100
10.730.9990.03922.695752061680.04681.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2xmi


Resolution: 2.4→19.673 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.299 1646 10.04 %
Rwork0.2487 14750 -
obs0.2537 16396 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.53 Å2 / Biso mean: 46.1172 Å2 / Biso min: 3.77 Å2
Refinement stepCycle: final / Resolution: 2.4→19.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 14 141 3472
Biso mean--52.22 30.04 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023416
X-RAY DIFFRACTIONf_angle_d0.6284596
X-RAY DIFFRACTIONf_chiral_restr0.024494
X-RAY DIFFRACTIONf_plane_restr0.004584
X-RAY DIFFRACTIONf_dihedral_angle_d13.8351271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.47060.37521340.33971109124390
2.4706-2.55020.38111340.31611217135199
2.5502-2.64110.36011360.322512341370100
2.6411-2.74660.40751340.308312311365100
2.7466-2.87130.3531390.287212231362100
2.8713-3.02210.32681340.273512461380100
3.0221-3.21070.32671370.281812171354100
3.2107-3.45740.30091370.239812421379100
3.4574-3.80310.28431350.228212391374100
3.8031-4.34820.23611470.207512451392100
4.3482-5.45880.23141330.20331249138299
5.4588-19.6740.28121460.220112981444100
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)
13.51411.63231.39362.87711.09462.4097-0.04030.069-0.03260.05570.1262-0.0141-0.0431-0.0772-0.09630.1710.0007-0.01420.1980.0510.392141.87488.864345.1131
21.8835-0.35112.25061.23530.88043.9410.1950.2439-0.1713-0.12580.0423-0.18030.12450.4743-0.19770.22950.00180.05880.28730.05450.381744.31345.342437.6911
33.36190.1568-2.47513.16670.26344.3307-0.45910.2784-0.0181-0.04090.20420.06440.2973-0.44040.22430.2284-0.0106-0.07390.2001-0.010.175921.94513.06525.072
47.5413-6.31041.51358.35743.20966.89640.2046-0.36710.0773-0.534-0.6552-0.6146-0.5782-0.40070.30330.54820.1217-0.0220.35860.03610.90512.561633.434521.8908
52.39460.90472.34185.4016-2.48934.72480.4383-0.47440.62510.209-0.0746-0.149-0.2961-0.5616-0.2020.1158-0.02680.01860.2346-0.07720.479712.651226.41958.5433
66.6394.9074-0.40124.7791-0.20115.5969-0.3530.3509-0.1272-0.68880.5088-0.1610.13840.21570.01670.202-0.05170.00760.19830.01810.510934.872716.7144-0.3013
77.2902-1.41620.18761.41391.15752.2588-0.13020.6025-0.5004-0.39790.1703-0.63440.00760.0825-0.11620.40410.10640.03770.1825-0.03080.219240.21225.60671.5088
81.9249-0.0018-0.99710.53331.3463.9322-0.2948-0.13750.22730.1580.42470.0150.3862-0.1398-0.07240.1764-0.0109-0.04510.1453-0.01360.234823.781815.926714.5179
94.405-1.60340.83358.07095.64584.8943-0.07650.0520.6188-0.47940.6502-0.3535-0.83820.5767-0.4130.56570.0499-0.0890.2207-0.02930.467837.901110.679812.2113
101.4171-1.17340.4810.99-0.67864.1653-0.06780.18340.0001-0.04350.0461-0.3118-0.5860.45020.22550.1673-0.0165-0.1350.2675-0.07580.611229.281222.015611.3566
112.4355-2.47510.62696.9191-1.65822.49720.1226-0.29080.37360.20410.0628-1.0568-0.19240.14040.11640.24180.0086-0.09670.22040.00440.871729.775525.032516.5751
128.25885.636-6.49416.8722-4.60335.13330.1493-1.2224-0.1419-0.0228-0.33160.24610.27381.2856-0.0080.46850.0397-0.09560.4934-0.04750.426919.334823.661926.3606
130.3452-0.7032-0.87321.94212.23734.08150.1194-0.0113-0.1363-0.05080.02560.0306-0.0499-0.5087-0.15620.1925-0.0054-0.0090.3242-0.00150.570723.26911.175111.9824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 288 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 289 through 378 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 160 through 194 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 195 through 205 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 229 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 230 through 243 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 244 through 259 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 280 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 281 through 297 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 298 through 319 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 320 through 336 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 337 through 358 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 359 through 378 )B0

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