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

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Basic information

Entry
Database: PDB / ID: 4wdb
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation R307Q, complexed with 2'-AMP
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: 1.6 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,6483
Polymers24,2651
Non-polymers3832
Water2,198122
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-17 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.880, 47.890, 107.410
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: 24264.863 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: R307Q
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): rosetta2
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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.06 Å3/Da / Density % sol: 40.31 %
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: 1.6→40 Å / Num. obs: 27315 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 26.23 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.057 / Χ2: 0.982 / Net I/σ(I): 18.82 / Num. measured all: 194176
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
1.6-1.646.80.3441.8690.9913555199119912.025100
1.64-1.690.6031.3011.4713459192419231.40699.9
1.69-1.740.6981.0531.8613872187018691.13299.9
1.74-1.790.7970.7892.4913548184318420.84999.9
1.79-1.850.8750.5643.3912963179017900.608100
1.85-1.910.9170.4174.5812103171217120.45100
1.91-1.980.9620.2796.6811323165916580.30299.9
1.98-2.070.9790.2138.9711798161316120.22999.9
2.07-2.160.9890.1512.6511414153615360.161100
2.16-2.260.9940.1116.710830146714670.118100
2.26-2.390.9960.09119.7710154141414140.098100
2.39-2.530.9970.07622.329060132913290.083100
2.53-2.70.9980.05730.399279126212620.061100
2.7-2.920.9990.04537.538807118111810.048100
2.92-3.20.9990.03545.367912109810970.03899.9
3.2-3.580.9990.02953.3864749929910.03299.9
3.58-4.130.9990.02464.2561948968960.026100
4.13-5.060.9990.02170.852847567540.02399.7
5.06-7.160.9990.02263.5438606156150.024100
7.1610.0266.1822873803760.02298.9

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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: 1.6→35.743 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 1363 5 %
Rwork0.1651 25890 -
obs0.167 27253 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.72 Å2 / Biso mean: 43.5815 Å2 / Biso min: 17.52 Å2
Refinement stepCycle: final / Resolution: 1.6→35.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 71 123 1846
Biso mean--55.55 44.31 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171824
X-RAY DIFFRACTIONf_angle_d1.7582478
X-RAY DIFFRACTIONf_chiral_restr0.08265
X-RAY DIFFRACTIONf_plane_restr0.01313
X-RAY DIFFRACTIONf_dihedral_angle_d20.307690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5998-1.6570.35611340.330325612695
1.657-1.72340.26681340.260925272661
1.7234-1.80180.24461330.225525422675
1.8018-1.89680.24611340.195225402674
1.8968-2.01560.24311360.177825732709
2.0156-2.17120.18931350.152925732708
2.1712-2.38970.20431360.146125792715
2.3897-2.73530.18271360.148425922728
2.7353-3.44580.19211400.155626482788
3.4458-35.7520.18961450.15827552900
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)
13.62460.37810.50172.5958-0.36222.7425-0.36960.57850.2497-0.55860.18840.4017-0.2466-0.11940.19460.246-0.0312-0.04750.24670.01510.2576-10.906815.1009-29.9375
21.8436-2.55461.2376.1806-3.11323.57990.02210.02930.25870.1678-0.2839-0.70760.02890.50640.19520.2264-0.0179-0.0830.32630.01560.37369.441110.1004-14.6767
32.603-1.6217-1.38582.8755-0.63565.5179-0.0812-0.1278-0.50720.1320.3083-0.02221.30810.3976-0.290.56970.0632-0.13950.40230.06250.484910.409-7.7895-6.8234
40.5781-0.41350.13831.7917-1.28361.1794-0.01670.1195-0.0325-0.0864-0.048-0.0440.25960.19670.05530.27770.00790.00240.2489-0.03840.2328-3.25875.5495-24.2236
55.13350.1664-0.74543.1543-1.18742.709-0.0833-0.0580.0977-0.18160.0460.6079-0.3674-0.56740.09770.23410.0705-0.03630.26690.00160.3663-17.819519.9927-25.4427
61.8887-0.70740.50871.3597-0.89541.1448-0.0223-0.16520.02550.30680.03570.04510.01010.0193-0.05270.2524-0.005-0.02180.2472-0.03040.2145-2.11049.4321-12.1378
73.71880.50750.70123.6431-1.00394.30150.0810.0165-0.21780.06280.05070.55680.0622-0.5074-0.08140.23740.02060.01150.3092-0.04830.3007-15.528913.1594-15.1363
81.9719-1.7013-0.0511.53720.16851.6383-0.05370.0648-0.3890.2966-0.03440.30360.3973-0.28770.09510.272-0.03480.02950.248-0.03220.3171-8.55523.0851-15.2106
95.2361-0.570.04946.10821.38027.6347-0.0384-0.3585-0.53940.1350.03940.35650.1448-0.5314-0.04290.30390.02140.0220.31770.00320.2729-8.34490.6928-11.4188
101.112-0.37961.64044.04830.59242.760.1114-0.3345-0.02861.0367-0.0349-0.06550.40510.0519-0.17860.5968-0.0494-0.08780.48830.00050.23022.84193.00721.1999
111.66131.20960.34667.13361.59742.61260.1386-0.53230.26820.5266-0.50410.466-0.0255-0.09330.30480.4166-0.0244-0.06810.352-0.03090.27370.67984.3232-4.3099
124.96921.01632.43273.4187-0.77463.2187-0.0990.05230.102-0.2080.2762-0.2179-0.27490.0963-0.23180.2126-0.02480.02740.232-0.02380.3008-4.152717.9872-22.9658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 174 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 193 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 216 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 243 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 259 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 279 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 280 through 296 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 297 through 319 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 320 through 335 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 336 through 355 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 356 through 366 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 367 through 378 )A0

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