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

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Basic information

Entry
Database: PDB / ID: 4wfr
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation T232A, complexed with 2'-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
ADENOSINE-2'-MONOPHOSPHATE / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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)24,6112
Polymers24,2641
Non-polymers3471
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-6 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.770, 47.094, 53.951
Angle α, β, γ (deg.)90.000, 94.360, 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: 24263.900 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 159-378 / Mutation: T232A
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: Chemical ChemComp-2AM / ADENOSINE-2'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
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: MAX II / Beamline: I911-2 / Wavelength: 1.04088 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04088 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 13864 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 19.29 Å2 / Rmerge F obs: 0.993 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.135 / Χ2: 0.923 / Net I/σ(I): 9.62 / Num. measured all: 45554
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
2-2.053.20.5050.5312.313267104910080.63696.1
2.05-2.110.6860.3543.7315010089750.42596.7
2.11-2.170.6750.3723.37321310069780.44597.2
2.17-2.240.7560.4053.1831199709400.48596.9
2.24-2.310.8680.3334.0129449429080.496.4
2.31-2.390.850.3943.4128468788560.47197.5
2.39-2.480.8970.3213.928648828620.38397.7
2.48-2.580.8890.2814.4827948478390.33699.1
2.58-2.70.9270.2465.1225778037860.29797.9
2.7-2.830.9480.2046.1525317807600.24597.4
2.83-2.980.9660.1577.7624307607380.18997.1
2.98-3.160.9810.11110.9821926786670.13398.4
3.16-3.380.9890.06616.5221736696590.07998.5
3.38-3.650.9920.05719.9919276055840.06896.5
3.65-40.9950.04822.9217685705490.05896.3
4-4.470.9960.03926.8516615275130.04697.3
4.47-5.160.9970.03529.0914124534320.04195.4
5.16-6.320.9970.03726.2712403863720.04496.4
6.32-8.940.9980.03129.979743082900.03794.2
8.940.9990.02438.724721771480.02983.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å34.21 Å
Translation3.5 Å34.21 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xmi

2xmi


Resolution: 2→34.214 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2663 693 5 %
Rwork0.2161 13168 -
obs0.2186 13861 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.85 Å2 / Biso mean: 34.8745 Å2 / Biso min: 6.07 Å2
Refinement stepCycle: final / Resolution: 2→34.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 35 109 1738
Biso mean--46.72 29.17 -
Num. residues----204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031670
X-RAY DIFFRACTIONf_angle_d0.8232253
X-RAY DIFFRACTIONf_chiral_restr0.032244
X-RAY DIFFRACTIONf_plane_restr0.004281
X-RAY DIFFRACTIONf_dihedral_angle_d15.416620
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 (%)
2-2.15440.35021360.28062575271196
2.1544-2.37120.30061380.26342625276397
2.3712-2.71410.31971400.25012660280098
2.7141-3.4190.24941400.21182658279898
3.419-34.21940.21971390.17282650278996
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)
12.7823-0.438-0.26382.9896-0.30571.6325-0.3595-0.36650.0650.42320.3034-0.3589-0.2107-0.10130.05670.11890.0634-0.05090.1109-0.02780.18150.307514.704628.8132
22.72052.77822.02863.76423.64244.9545-0.1811-0.0860.3582-0.2329-0.01370.8471-0.0911-0.57680.18130.1920.0068-0.06690.24570.04350.253330.401510.964614.7874
36.0945-0.6385-1.65781.5174-1.22546.0468-0.03050.3616-0.8899-0.7554-0.0820.30920.5378-0.53980.46690.7009-0.172-0.13090.36440.00430.364829.1384-7.67257.38
41.28631.4705-0.02381.83430.33890.8412-0.01770.01330.0850.0499-0.03930.10760.234-0.16380.0580.1585-0.010.01930.1734-0.00460.122743.01045.610524.2336
53.06571.1669-0.47111.83320.80140.7653-0.0935-0.33390.15920.4311-0.0034-0.9062-0.11720.20690.03720.2116-0.0774-0.07080.24780.00830.35558.752519.008925.8099
61.44921.2463-0.29182.2249-0.23731.6292-0.10780.0655-0.0921-0.32240.0906-0.42010.06690.19710.04530.1253-0.02660.03960.1659-0.01920.160347.52288.737914.1269
75.2732-2.14363.11533.2803-1.40652.99310.04680.49380.3652-0.9518-0.0432-0.52420.43230.1565-0.00410.3881-0.10420.05610.24930.01520.305642.61642.4596.3606
81.40540.53070.82182.92120.72382.3069-0.19130.1770.023-0.6430.1728-0.0031-0.1095-0.07020.00280.2084-0.05590.07960.1911-0.01050.198440.54579.795911.1887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 174 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 193 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 216 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 243 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 259 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 319 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 348 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 349 through 378 )A0

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