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

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Basic information

Entry
Database: PDB / ID: 4wdf
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation V321A, complexed with 2',5'-ADP
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
ADENOSINE-2'-5'-DIPHOSPHATE / 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 8, 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)24,6932
Polymers24,2661
Non-polymers4271
Water1,24369
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-5 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.090, 47.010, 53.650
Angle α, β, γ (deg.)90.000, 95.670, 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: 24265.875 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 179-378 / Mutation: V321A
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-A2P / ADENOSINE-2'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.12 Å3/Da / Density % sol: 42.12 %
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: P13 (MX1) / Wavelength: 1.03149 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03149 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 13871 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 36.38 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.098 / Χ2: 0.95 / Net I/σ(I): 9.28 / Num. measured all: 49831
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
2-2.053.60.3810.9421.453763103510341.10199.9
2.05-2.110.5450.7931.8234839839700.92898.7
2.11-2.170.6050.6392.1934819919900.75299.9
2.17-2.240.7130.5382.6131759499430.6499.4
2.24-2.310.8580.4173.4131789049010.49199.7
2.31-2.390.8410.3883.8832448888820.45299.3
2.39-2.480.9170.2964.730628358350.347100
2.48-2.580.9350.2495.8830618448400.29299.5
2.58-2.70.9680.1886.7626427697690.222100
2.7-2.830.9790.158.6727627697660.17699.6
2.83-2.980.9870.10911.2126917137090.12699.4
2.98-3.160.9920.08513.2725946976920.09999.3
3.16-3.380.9950.06916.4223056336320.0899.8
3.38-3.650.9940.05918.8220245935840.0798.5
3.65-40.9960.0522.1120615495420.05898.7
4-4.470.9960.04324.519165155130.0599.6
4.47-5.160.9950.04624.0414934434370.05498.6
5.16-6.320.9950.04923.5613303723690.05899.2
6.32-8.940.9950.04724.3510293032960.05697.7
8.940.9950.04524.75371721670.05397.1

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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→35.281 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1385 9.99 %
Rwork0.2035 12473 -
obs0.209 13858 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.25 Å2 / Biso mean: 59.4803 Å2 / Biso min: 21.68 Å2
Refinement stepCycle: final / Resolution: 2→35.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 38 69 1759
Biso mean--81.22 52.5 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051728
X-RAY DIFFRACTIONf_angle_d0.8982335
X-RAY DIFFRACTIONf_chiral_restr0.033250
X-RAY DIFFRACTIONf_plane_restr0.003294
X-RAY DIFFRACTIONf_dihedral_angle_d14.59631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.07160.37261390.308912561395100
2.0716-2.15450.36381390.291212431382100
2.1545-2.25260.33061360.26241223135999
2.2526-2.37130.26391370.23712331370100
2.3713-2.51990.28791360.224212251361100
2.5199-2.71430.26411420.21712741416100
2.7143-2.98740.28941350.217512341369100
2.9874-3.41930.2421400.197412571397100
3.4193-4.30680.22911390.17721246138599
4.3068-35.2870.23371420.1771282142499
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)
13.76781.47651.37242.90570.18832.5868-0.10770.0316-0.2117-0.20510.1509-0.11370.0529-0.1802-0.03850.2660.04340.06470.2474-0.01480.273934.50736.426972.685
22.23811.66590.30963.92780.77053.193-0.32940.3699-0.3218-0.91070.3132-0.47580.12530.09940.00680.4176-0.03160.11250.3121-0.02040.355538.58346.260964.5015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 163 through 259 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 260 through 378 )A0

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