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

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Basic information

Entry
Database: PDB / ID: 4wcb
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation 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: 1.57 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 1.1Jan 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

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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)24,3192
Polymers24,2841
Non-polymers351
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.810, 48.270, 108.060
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: 24283.910 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): Rosetta
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 304 / 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-acetate, PEG 4000/6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04088 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04088 Å / Relative weight: 1
ReflectionResolution: 1.57→30 Å / Num. obs: 29179 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 15.79 Å2 / Rmerge F obs: 0.112 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.076 / Χ2: 0.983 / Net I/σ(I): 18.18 / Num. measured all: 200891
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.57-1.610.790.9382.1412993215921471.03299.4
1.61-1.650.6390.7632.6113522203520350.829100
1.65-1.70.5060.5653.4513515201520140.613100
1.7-1.760.40.4734.1913398195619540.51299.9
1.76-1.810.3240.3745.2513234189018890.40499.9
1.81-1.880.2710.3066.4813144186718670.33100
1.88-1.950.1890.2348.312582177517750.252100
1.95-2.030.1260.16411.8212210170817080.176100
2.03-2.120.0930.12614.9811716164816470.13699.9
2.12-2.220.0720.09918.9911132156715670.106100
2.22-2.340.0670.08821.8710706150915080.09599.9
2.34-2.480.0560.07424.9410213143314330.08100
2.48-2.650.0450.06527.739631135013500.07100
2.65-2.870.0390.05331.938827125812580.058100
2.87-3.140.0310.04437.28116116511650.048100
3.14-3.510.0210.03646.617297107810750.03999.7
3.51-4.050.0170.0353.3164739459420.03299.7
4.05-4.960.0130.02359.1155888198170.02599.8
4.96-7.020.0160.02454.4544126536530.026100
7.020.0150.0253.6121824013750.02293.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSDecember 31, 2011data reduction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xmi

2xmi


Resolution: 1.57→28.868 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 1456 5 %
Rwork0.1588 27662 -
obs0.1611 29118 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.63 Å2 / Biso mean: 24.9192 Å2 / Biso min: 8.05 Å2
Refinement stepCycle: final / Resolution: 1.57→28.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 1 304 1967
Biso mean--19.68 32.88 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071741
X-RAY DIFFRACTIONf_angle_d1.0832349
X-RAY DIFFRACTIONf_chiral_restr0.042252
X-RAY DIFFRACTIONf_plane_restr0.006302
X-RAY DIFFRACTIONf_dihedral_angle_d13.812657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5701-1.62630.29041430.25592738288199
1.6263-1.69140.251430.217827122855100
1.6914-1.76830.26251440.193427322876100
1.7683-1.86150.2321430.186227282871100
1.8615-1.97820.20571420.168427122854100
1.9782-2.13080.21031450.149627502895100
2.1308-2.34520.19161450.144627682913100
2.3452-2.68430.20631470.151527862933100
2.6843-3.38110.19021480.145728052953100
3.3811-28.87320.18361560.14632931308799
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)
10.0136-0.013-0.01930.05920.00080.0308-0.1440.11550.106-0.03050.04750.0859-0.0532-0.0335-0.00090.071-0.0133-0.02640.1336-0.00010.1243-10.12114.7807-28.9649
20.0272-0.0057-0.01540.00870.01040.0113-0.01380.06540.10730.0247-0.0449-0.0810.01810.1085-0.00230.12360.0073-0.05720.14850.01870.18029.76719.147-14.1015
30.2980.04820.08380.125-0.10640.2501-0.014-0.0102-0.2110.07-0.0104-0.02460.16990.1818-0.03580.24770.0542-0.10.12790.05770.21139.9724-9.3475-7.7663
40.0310.0161-0.00150.0538-0.06540.0421-0.07080.01370.0020.01670.03050.04020.07650.0428-0.00970.09430.01490.00040.1095-0.01090.1164-3.67675.6424-24.5698
50.0147-0.010.01420.0075-0.02070.0499-0.00330.03590.0036-0.06520.0370.1672-0.1386-0.09140.01650.09360.0212-0.01130.10620.00410.1369-18.027120.3257-25.3855
60.08970.0278-0.04490.0094-0.01820.0422-0.049-0.04740.00250.06350.0020.0143-0.06020.0185-0.00670.14820.0092-0.01770.1187-0.01060.0962-2.09138.9981-12.4311
70.0655-0.00750.00390.0192-0.01040.0370.0771-0.0367-0.12430.23310.07960.062-0.0236-0.09940.05160.11440.01830.01390.1426-0.01210.132-15.451613.4515-15.1853
80.03240.01040.00090.1027-0.05460.07140.07190.0788-0.06250.0233-0.03110.09010.0185-0.08580.02270.10260.0004-0.00010.1298-0.00820.1098-8.26073.2722-15.0864
9-0.0001-0.00030.00170.0237-0.0040.0042-0.0359-0.0453-0.08470.02350.02040.08950.0096-0.014-00.1140.00290.0160.13860.00360.1165-8.52840.534-10.1707
100.0620.00480.04720.0266-0.01660.0387-0.0296-0.09640.03960.1157-0.0270.0116-0.0617-0.1043-0.07040.3928-0.0501-0.14070.17970.0293-0.0142.7532.68180.9827
110.1289-0.0112-0.02220.0259-0.02890.0252-0.0508-0.00560.05050.08120.031-0.1157-0.0228-0.03810.01810.1474-0.0017-0.02940.1021-0.01030.1003-1.568711.5658-13.7662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 174 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 194 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 195 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 378 )A0

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