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

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Basic information

Entry
Database: PDB / ID: 4wdh
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation Y168A
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
ACETIC ACID / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 30, 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)24,3334
Polymers24,2021
Non-polymers1313
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.310, 48.330, 54.030
Angle α, β, γ (deg.)90.000, 94.520, 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: 24201.830 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 179-398 / Mutation: Y168A
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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
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 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.223 Å / Relative weight: 1
ReflectionResolution: 1.9→60 Å / Num. obs: 14974 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 23.65 Å2 / Rmerge F obs: 0.15 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.083 / Χ2: 0.982 / Net I/σ(I): 9.49 / Num. measured all: 42879
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
1.9-1.951.81.3060.7221.27155511758500.92772.3
1.95-20.9750.581.692203117110050.72385.8
2-2.060.750.472.22234611169960.58189.2
2.06-2.120.4590.3323.12229510699590.40989.7
2.12-2.190.3960.2683.67239610699650.3390.3
2.19-2.270.3480.234.45237810049210.28491.7
2.27-2.360.3340.24.8324329979250.24792.8
2.36-2.450.2790.1745.5924789519070.21395.4
2.45-2.560.2570.1646.3325049048740.296.7
2.56-2.690.2110.137.8825398858590.15897.1
2.69-2.830.1510.1029.6225438368200.12398.1
2.83-30.1140.08911.6525247817760.10799.4
3-3.210.0730.0715.0925317397380.08399.9
3.21-3.470.0450.05519.8624446896830.06599.1
3.47-3.80.0410.0521.5522836336300.05999.5
3.8-4.250.0380.05123.7421145815790.0699.7
4.25-4.910.0350.04923.7818435185160.05799.6
4.91-6.010.0320.04323.3815614344310.0599.3
6.01-8.50.0290.03724.0512253423400.04399.4
8.50.0240.03425.696852022000.0499

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xmi

2xmi


Resolution: 1.9→53.862 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 30.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 748 5 %
Rwork0.2168 14204 -
obs0.2189 14952 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.25 Å2 / Biso mean: 43.8576 Å2 / Biso min: 13.57 Å2
Refinement stepCycle: final / Resolution: 1.9→53.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 9 153 1820
Biso mean--44.14 37.43 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031720
X-RAY DIFFRACTIONf_angle_d0.7142318
X-RAY DIFFRACTIONf_chiral_restr0.027250
X-RAY DIFFRACTIONf_plane_restr0.004297
X-RAY DIFFRACTIONf_dihedral_angle_d14.376645
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 (%)
1.9003-2.0470.3781300.31912460259082
2.047-2.2530.32051440.26962743288790
2.253-2.5790.30721530.25912895304895
2.579-3.24920.28731580.23353007316599
3.2492-53.8840.20081630.16923099326299
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)
13.80831.82731.58654.22511.40742.60270.0685-0.23110.2259-0.1732-0.11920.29640.2928-0.42010.14650.1913-0.0131-0.01440.18020.00670.16535.165612.156420.3027
26.5148-2.85462.29833.44032.18235.7021-0.19110.2459-1.3019-0.57040.37421.00751.4481-0.98320.57021.1709-0.2958-0.05190.3568-0.1170.495427.1043-9.89138.0702
31.1550.9547-0.00523.09990.0682.1645-0.1742-0.07240.0236-0.01820.0329-0.34790.05260.10090.14050.15240.01260.01390.1615-0.01030.229746.750111.649524.7918
45.84025.79923.24876.52182.26115.5104-0.4210.11560.0592-1.36240.2398-0.47290.05320.0520.24970.2915-0.01950.0560.1701-0.01350.230939.482113.950111.8522
55.76424.44891.40853.33821.22671.903-0.1730.349-0.4365-0.21670.3464-0.6286-0.04140.356-0.13450.2801-0.03130.0770.2605-0.02770.292549.30649.268214.1847
62.74141.5695-0.37842.8055-0.48152.7819-0.12020.1853-0.4628-0.71660.0265-0.31980.20740.2250.00120.4117-0.03580.0670.2245-0.06090.270341.97512.679710.1561
72.13021.40140.72753.60661.80484.3617-0.34340.37680.0453-0.53930.28120.0110.331-0.02780.12910.3209-0.04880.06570.23450.00940.211537.99629.377711.035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 163 through 193 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 194 through 216 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 259 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 270 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 271 through 299 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 348 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 349 through 378 )A0

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