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

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Basic information

Entry
Database: PDB / ID: 4wdd
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation T232A, 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 / 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
CITRIC ACID / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 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 30, 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)24,6195
Polymers24,2641
Non-polymers3554
Water1,08160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-19 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.230, 46.030, 106.680
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: 24263.900 Da / Num. of mol.: 1 / Fragment: catalytic domain, unp residues 179-398 / Mutation: 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) / Variant (production host): rosetta2
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-citrate, 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 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 12659 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 32.7 Å2 / Rmerge F obs: 0.239 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.155 / Χ2: 0.969 / Net I/σ(I): 9.77 / Num. measured all: 71976
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
2.1-2.165.60.8540.9191.7751399199191.015100
2.16-2.210.8070.856251458968960.942100
2.21-2.280.8240.872.148818558550.959100
2.28-2.350.9090.9392.1149618578571.034100
2.35-2.430.8060.8432.4948258368350.92899.9
2.43-2.510.8140.8992.5745497797790.989100
2.51-2.610.6390.7463.2746047887880.821100
2.61-2.710.5610.6044.1242787347340.664100
2.71-2.830.4350.5095.4741967237230.559100
2.83-2.970.3610.4376.7939156786760.4899.7
2.97-3.130.2140.2728.9137816596580.29999.8
3.13-3.320.10.13613.2235636236220.1599.8
3.32-3.550.0640.10117.6432935865840.11299.7
3.55-3.840.0550.07820.5531285565540.08699.6
3.84-4.20.050.06124.4727725065040.06899.6
4.2-4.70.0410.05228.4624554644600.05899.1
4.7-5.420.0380.05129.5922604134130.056100
5.42-6.640.0320.04329.4419593573570.048100
6.64-9.40.0260.03632.2815162882880.041100
9.40.0230.03133.367561791570.03587.7

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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: 2.101→19.856 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 633 5 %
Rwork0.2127 12022 -
obs0.2155 12655 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.66 Å2 / Biso mean: 57.4465 Å2 / Biso min: 19.73 Å2
Refinement stepCycle: final / Resolution: 2.101→19.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 34 60 1707
Biso mean--65.91 46.04 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031699
X-RAY DIFFRACTIONf_angle_d0.6412288
X-RAY DIFFRACTIONf_chiral_restr0.026241
X-RAY DIFFRACTIONf_plane_restr0.003294
X-RAY DIFFRACTIONf_dihedral_angle_d14.713636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.101-2.2630.34531230.306623392462
2.263-2.49030.36461250.275423862511
2.4903-2.84970.2871260.249323802506
2.8497-3.58690.25671260.207623982524
3.5869-19.85650.23641330.174425192652
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)
15.1959-1.52511.58995.6761-1.4373.45610.0174-0.167-0.20350.61460.152-0.55810.24630.5807-0.11720.43030.0475-0.05490.2786-0.10360.30894.42674.7305-15.6943
21.2826-2.0380.58615.0002-0.55051.93070.16980.2441-0.2155-0.223-0.14610.3730.06310.03680.0010.259-0.0250.01120.2029-0.01250.3875-9.599510.1216-24.5815
33.861-1.12851.06323.9395-0.30390.9904-0.1846-0.4872-0.14660.95270.1860.59270.0523-0.25-0.03390.45440.07450.11610.2960.04970.2937-7.97387.2822-13.7017
43.3354-1.12481.23493.7719-2.03653.8595-0.1872-0.71280.02011.31220.2224-0.12810.0303-0.07510.02450.77210.0702-0.04550.4012-0.02880.3630.1187.8136-7.5471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 216 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 217 through 256 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 336 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 337 through 378 )A0

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