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

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Basic information

Entry
Database: PDB / ID: 4wbi
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutations H230Q and H309Q
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 / 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 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)24,2901
Polymers24,2901
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.130, 47.030, 108.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein 2',3'-cyclic-nucleotide 3'-phosphodiesterase / CNPase


Mass: 24289.891 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 179-398 / Mutation: H230Q, H309Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.01 %
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: 1.04002 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04002 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 14675 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 32.65 Å2 / Rmerge F obs: 0.12 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.08 / Χ2: 0.93 / Net I/σ(I): 14.52 / Num. measured all: 87766
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
2-2.055.90.7190.812.236269108610660.88698.2
2.05-2.110.530.613.046004102410000.66697.7
2.11-2.170.420.53.676109103710190.54698.3
2.17-2.240.380.414.5359219949810.44898.7
2.24-2.310.3480.3584.9957629599460.39198.6
2.31-2.390.2890.3195.6255279169100.34899.3
2.39-2.480.2620.2636.7255309069010.28899.4
2.48-2.580.1960.2058.1253308788730.22499.4
2.58-2.70.1620.16610.0350548248210.18199.6
2.7-2.830.1270.13511.9349278048020.14799.8
2.83-2.980.1050.10514.0146917747740.115100
2.98-3.160.0620.07818.5243957267260.086100
3.16-3.380.0390.05925.1941226816780.06599.6
3.38-3.650.0320.04730.9537356376330.05299.4
3.65-40.0270.03935.2134925955920.04399.5
4-4.470.0210.03739.1731095455410.04199.3
4.47-5.160.0210.03439.8827564904890.03799.8
5.16-6.320.0230.03537.8923354104090.03899.8
6.32-8.940.020.03440.118383383340.03898.8
8.940.020.03240.828602001800.03690

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSDecember 29, 2011data 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→28.641 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 734 5 %
Rwork0.2006 13938 -
obs0.2021 14672 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.84 Å2 / Biso mean: 54.8745 Å2 / Biso min: 21.54 Å2
Refinement stepCycle: final / Resolution: 2→28.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 0 94 1716
Biso mean---46.06 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071655
X-RAY DIFFRACTIONf_angle_d0.9552224
X-RAY DIFFRACTIONf_chiral_restr0.035240
X-RAY DIFFRACTIONf_plane_restr0.004282
X-RAY DIFFRACTIONf_dihedral_angle_d14.795618
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 (%)
2-2.15440.30961430.27992715285898
2.1544-2.37110.29351430.23992726286999
2.3711-2.7140.2781460.23342771291799
2.714-3.41840.25271480.207828062954100
3.4184-28.64430.18481540.16872920307499
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)
14.6487-2.19821.96644.5689-1.28863.0622-0.1154-0.1033-0.22830.38630.13350.05350.06710.22440.01010.2699-0.01480.0880.2345-0.01550.2103-1.34656.5043-19.7128
22.1115-1.23140.1214.0194-0.96382.8491-0.171-0.3719-0.2140.9840.14790.4529-0.0893-0.1105-0.04770.4964-0.00710.13170.3050.02290.3004-5.07965.619-10.1954
33.2277-2.14892.11393.6578-2.47785.1206-0.2828-0.39640.21460.9810.2180.0451-0.4777-0.04560.13110.4779-0.03350.10650.3475-0.05090.3222-1.646611.1402-14.0172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 259 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 260 through 355 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 356 through 378 )A0

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