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- PDB-2y1p: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -

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Basic information

Entry
Database: PDB / ID: 2y1p
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, complexed with citrate
Components2', 3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE
KeywordsHYDROLASE / MYELIN
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: 1.82 Å
AuthorsMyllykoski, M. / Kursula, P.
CitationJournal: Plos One / Year: 2012
Title: Myelin 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase: Active-Site Ligand Binding and Molecular Conformation.
Authors: Myllykoski, M. / Raasakka, A. / Han, H. / Kursula, P.
History
DepositionDec 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)24,5783
Polymers24,2941
Non-polymers2842
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.950, 46.920, 54.850
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2', 3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE / CNP / CNPASE


Mass: 24293.928 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 159-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PTH 27 / Production host: ESCHERICHIA COLI (E. coli) / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: NONE
Crystal growpH: 3.3 / Details: pH 3.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.82→26.28 Å / Num. obs: 19148 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.74 % / Biso Wilson estimate: 19.52 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.19
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.02 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMI

2xmi


Resolution: 1.82→26.283 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 957 5 %
Rwork0.1579 --
obs0.16 19146 99.7 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.915 Å2 / ksol: 0.431 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-0.1215 Å20 Å2-0.6288 Å2
2---1.6933 Å2-0 Å2
3---1.5718 Å2
Refinement stepCycle: LAST / Resolution: 1.82→26.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 19 215 1931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091761
X-RAY DIFFRACTIONf_angle_d1.1262375
X-RAY DIFFRACTIONf_dihedral_angle_d13.368662
X-RAY DIFFRACTIONf_chiral_restr0.078253
X-RAY DIFFRACTIONf_plane_restr0.006304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.91590.27871360.23182581X-RAY DIFFRACTION100
1.9159-2.03590.23571360.18352579X-RAY DIFFRACTION100
2.0359-2.1930.21631360.15662596X-RAY DIFFRACTION100
2.193-2.41360.20881360.14712577X-RAY DIFFRACTION100
2.4136-2.76250.20541370.15662601X-RAY DIFFRACTION100
2.7625-3.47920.19371370.152602X-RAY DIFFRACTION100
3.4792-26.28610.16951390.14852653X-RAY DIFFRACTION99
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)
11.0948-0.031-0.01050.49160.27940.4731-0.12720.03230.05420.05510.0861-0.0328-0.02560.11440.00410.0666-0.0050.00870.0879-0.01450.084323.2732-1.489110.2392
21.21320.21870.46610.53960.40720.86440.23830.1434-0.07030.23540.0607-0.13950.20730.2627-0.23240.16910.0454-0.0760.16-0.06120.165932.7941-16.372112.721
30.48790.3194-0.06980.32560.00270.485-0.14060.01690.0309-0.07090.02930.02180.10660.04730.05450.1208-0.0030.03810.08940.01170.114612.47880.52370.3636
40.859-0.70940.19941.734-0.10860.6847-0.1049-0.115-0.00220.15510.10120.1658-0.0983-0.0859-0.00350.07430.01470.02220.0829-0.01110.09379.90747.227210.0018
50.90810.37282.48290.54660.28148.16250.7202-0.2154-0.91150.14020.8228-0.2368-0.64370.2545-1.29110.2791-0.02250.23660.40140.03880.87680.3488-5.828512.6293
60.6896-0.29150.01260.1484-0.00380.2808-0.03860.0073-0.16630.02670.03560.13150.0243-0.01940.00310.09730.01850.05810.09720.0120.129313.8787-5.830114.6594
74.12791.9099-0.71976.6222-0.20180.1762-0.2179-0.76150.05931.03220.24530.16260.08350.2077-0.0190.31930.11490.00290.28050.01330.099523.795-6.014725.5605
81.38830.63841.41110.85961.65093.5296-0.0966-0.00610.28070.17310.0168-0.04430.19570.13320.03230.1277-0.0075-0.01030.0844-0.00840.131318.13138.767110.2585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 160:206)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 207:221)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 222:245)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 246:291)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 292:301)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 302:339)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 340:361)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 362:379)

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