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

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Basic information

Entry
Database: PDB / ID: 4wca
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H230Q, complexed with citrate
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
CITRIC ACID / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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)25,9579
Polymers24,3001
Non-polymers1,6578
Water2,486138
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.430, 47.640, 107.650
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: 24299.908 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 179-378 / Mutation: H230Q
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
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: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 18374 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 20.79 Å2 / Rmerge F obs: 0.129 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.092 / Χ2: 0.955 / Net I/σ(I): 15.6 / Num. measured all: 118188
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
1.85-1.940.9180.7131.835270132213100.82199.1
1.9-1.950.620.552.916613130413010.61599.8
1.95-2.010.4280.463.97824127312720.50399.9
2.01-2.070.3550.4094.597820122712260.44699.9
2.07-2.140.2730.2996.37910120712060.32599.9
2.14-2.210.1940.247.947693114211420.26100
2.21-2.290.1720.2059.517759113011300.222100
2.29-2.390.1430.18610.567587108610860.202100
2.39-2.490.1330.1612.17324103610360.172100
2.49-2.620.1070.1413.5169799939930.152100
2.62-2.760.0920.11316.1366829529520.122100
2.76-2.930.0670.08719.6562558918910.094100
2.93-3.130.0530.06923.9460448698670.07499.8
3.13-3.380.040.05231.0155017967960.056100
3.38-3.70.0310.04434.9950557407400.048100
3.7-4.140.0250.03841.145286666660.041100
4.14-4.780.0220.03644.4139996026020.039100
4.78-5.850.0260.04140.2333575165160.045100
5.85-8.270.0230.03338.1826894164160.036100
8.270.0160.02244.8712992482250.02490.7

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Processing

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

2xmi


Resolution: 1.85→19.619 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 919 5 %
Rwork0.1631 17455 -
obs0.1653 18374 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.04 Å2 / Biso mean: 33.2276 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: final / Resolution: 1.85→19.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1618 0 129 138 1885
Biso mean--49.23 37.51 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081751
X-RAY DIFFRACTIONf_angle_d1.082344
X-RAY DIFFRACTIONf_chiral_restr0.041246
X-RAY DIFFRACTIONf_plane_restr0.005297
X-RAY DIFFRACTIONf_dihedral_angle_d14.626671
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.94750.27781270.23782426255399
1.9475-2.06940.26261290.197324452574100
2.0694-2.2290.21191310.168524672598100
2.229-2.45290.19871280.159624582586100
2.4529-2.8070.21471320.159725032635100
2.807-3.53310.2181320.146425042636100
3.5331-19.62060.17861400.15426522792100
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)
13.1025-1.62770.92763.9226-2.13891.9189-0.1140.34510.36970.0754-0.158-0.2656-0.16340.30410.25960.1273-0.01420.01390.1235-0.010.10480.186613.0987-21.4438
25.813-3.78861.32925.6887-0.45872.4154-0.2219-0.455-0.74850.46530.22940.40131.23640.29770.04970.56470.0701-0.06260.27720.04530.330110.6196-6.5036-7.0817
32.1853-2.46992.29262.8456-2.6253.14950.13130.2491-0.026-0.0596-0.146-0.0040.19180.09430.0350.1253-0.01550.03510.1533-0.03410.1261-4.09896.8149-24.3557
49.0919-2.0839-2.38188.1723-0.67314.0032-0.13590.12290.1481-0.20170.0690.8982-0.209-0.48530.09220.14310.0607-0.01060.16840.04220.1646-18.198721.0626-25.663
53.3085-2.54720.572.5273-1.51092.5896-0.098-0.1476-0.20390.39150.16980.4146-0.241-0.4201-0.0230.18750.02790.03330.2044-0.00470.1568-10.159911.5018-13.7904
63.0327-0.62330.39972.7038-0.2273.0951-0.0136-0.3264-0.14160.4333-0.06490.07520.0228-0.2220.05460.1919-0.03120.02510.12590.01920.1169-4.52013.3337-9.2983
71.4076-1.36092.01021.792-2.90744.8592-0.1767-0.0250.06860.22550.0931-0.0352-0.29760.07130.05570.1921-0.0315-0.0030.1542-0.02770.1686-1.92812.3069-13.5551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 193 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 194 through 216 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 243 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 259 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 260 through 299 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 355 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 356 through 378 )A0

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