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

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Basic information

Entry
Database: PDB / ID: 4wcc
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation P225G
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: 2.7 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 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: 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

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Assembly

Deposited unit
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6154
Polymers24,1971
Non-polymers4183
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-28 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.790, 46.510, 106.280
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: 24196.812 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 179-398 / Mutation: P225G
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-2AM / ADENOSINE-2'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#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.: 5 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97907 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 5828 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 56.13 Å2 / Rmerge F obs: 0.138 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.077 / Χ2: 0.955 / Net I/σ(I): 17.63 / Num. measured all: 25515
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
2.7-2.773.90.9490.7471.7616024214080.85896.9
2.77-2.850.7630.6032.4318584184150.68399.3
2.85-2.930.5260.4293.1318244144080.48598.6
2.93-3.020.4190.3384.1417243833830.383100
3.02-3.120.350.2655.1917663983960.29999.5
3.12-3.230.2440.2086.8916293633580.23598.6
3.23-3.350.1690.1310.0216243663660.146100
3.35-3.490.1360.11611.8514513343250.13197.3
3.49-3.640.1140.08216.1515483483480.093100
3.64-3.820.0960.06919.6413823173080.07897.2
3.82-4.030.0660.05223.2113042982970.05999.7
4.03-4.270.0410.04229.5513013002900.04796.7
4.27-4.560.0380.03334.8811712762690.03897.5
4.56-4.930.0370.03238.4410982512500.03699.6
4.93-5.40.050.03533.4710192412320.0496.3
5.4-6.040.0470.04131.659042232130.04695.5
6.04-6.970.0440.03534.828121981910.0496.5
6.97-8.540.020.02646.16971711640.0395.9
8.54-12.080.0170.01555.565311381330.01796.4
12.080.0140.01452.6727086740.01786

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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: 2.7→34.998 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 292 5.01 %
Rwork0.2222 5536 -
obs0.2244 5828 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.08 Å2 / Biso mean: 68.3427 Å2 / Biso min: 30.42 Å2
Refinement stepCycle: final / Resolution: 2.7→34.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 37 5 1641
Biso mean--55.58 42.61 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041658
X-RAY DIFFRACTIONf_angle_d0.7442233
X-RAY DIFFRACTIONf_chiral_restr0.027241
X-RAY DIFFRACTIONf_plane_restr0.004278
X-RAY DIFFRACTIONf_dihedral_angle_d13.712606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7002-3.40150.30961430.26322721286499
3.4015-35.00120.25141490.20712815296497
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)
10.50050.4721-1.46076.9757-1.43774.28420.08280.2734-0.01390.595-0.1024-0.5419-0.52511.00590.14120.38-0.13780.00780.3659-0.07140.47071.043411.6611-20.1203
27.9216-3.81713.40237.0791-1.68174.51710.1162-0.0426-0.01770.3755-0.0537-0.16670.14070.2264-0.08530.3464-0.05320.07520.3164-0.02820.3391-3.95615.5494-19.4023
34.0184-1.8330.48615.7918-2.08164.3568-0.1542-0.7632-0.23591.30790.24040.4456-0.0566-0.1652-0.05290.64320.00810.11490.4225-0.00260.4386-5.00226.8533-10.8926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 194 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 259 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 378 )A0

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