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

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Basic information

Entry
Database: PDB / ID: 2xmi
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 / 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 / cell projection / response to toxic substance / melanosome / myelin sheath / mitochondrial inner membrane / microtubule / mitochondrial outer membrane / response to lipopolysaccharide / 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
CITRATE ANION / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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
DepositionJul 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

Deposited unit
A: 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5753
Polymers24,2941
Non-polymers2812
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.620, 47.110, 107.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


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-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.19 Å3/Da / Density % sol: 43.8 % / Description: NONE
Crystal growpH: 3.5 / Details: pH 3.5

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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: 1.74→35 Å / Num. obs: 22280 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.95 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.68
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 6.09 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.08 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WOJ

1woj


Resolution: 1.74→32.862 Å / SU ML: 0.22 / σ(F): 2.01 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 1114 5 %
Rwork0.1779 --
obs0.1795 22280 99.9 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.092 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.9395 Å20 Å20 Å2
2---6.3624 Å20 Å2
3----0.5771 Å2
Refinement stepCycle: LAST / Resolution: 1.74→32.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 19 162 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061734
X-RAY DIFFRACTIONf_angle_d0.9382334
X-RAY DIFFRACTIONf_dihedral_angle_d12.324645
X-RAY DIFFRACTIONf_chiral_restr0.067251
X-RAY DIFFRACTIONf_plane_restr0.004297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7402-1.81930.34311350.27922577X-RAY DIFFRACTION100
1.8193-1.91530.28091370.23732603X-RAY DIFFRACTION100
1.9153-2.03520.2481370.18862600X-RAY DIFFRACTION100
2.0352-2.19240.21091390.16962631X-RAY DIFFRACTION100
2.1924-2.41290.19881370.16742607X-RAY DIFFRACTION100
2.4129-2.76190.21011400.17972660X-RAY DIFFRACTION100
2.7619-3.47910.20341410.16582676X-RAY DIFFRACTION100
3.4791-32.86760.18381480.16852812X-RAY DIFFRACTION100
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)
11.8203-0.4362-1.13530.38470.26890.6971-0.2731-0.1492-0.1970.19010.118-0.00620.30050.20050.09180.10270.03280.02660.14720.03080.1299-10.9183-15.341630.3659
22.31720.4574-0.26841.460.80520.9283-0.13750.1986-0.1041-0.68220.169-0.4542-0.09890.3561-0.0850.3054-0.09890.14980.2354-0.03930.18488.9464-2.12539.7751
33.37470.3081-0.28081.4967-1.18260.93720.0887-0.26880.9744-1.26260.3130.4318-1.2413-0.0733-0.31460.9006-0.01620.22810.3145-0.09070.655311.049414.373713.1913
40.28230.0831-0.06831.60340.03480.3402-0.09170.0644-0.0893-0.18260.06840.0383-0.0795-0.01830.00310.1125-0.0154-0.01160.1497-0.00860.1037-2.2555-4.923.0158
51.51361.1949-0.12084.525-0.13680.5951-0.20150.17710.046-0.610.21820.46350.1336-0.1178-0.03230.1208-0.0381-0.05270.1224-0.00260.1193-11.1368-15.163517.1667
60.3405-0.92740.96252.9092-3.68135.48410.84420.0131-0.2482-0.24310.18550.97290.12290.6199-0.82660.373-0.0528-0.18140.45-0.07050.6881-21.1852-3.011416.9205
71.60521.2387-0.72072.7122-0.25960.5975-0.14010.04530.1896-0.53020.27280.1814-0.0252-0.001-0.06780.1851-0.0444-0.05770.10110.03290.1264-8.107-1.75212.506
81.22270.4181-0.08073.50220.18190.3278-0.2740.2954-0.1335-1.21090.2842-0.16510.1013-0.090.02560.4174-0.0720.05850.1866-0.05250.0901-0.0021-8.17138.0155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 160:175)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 176:205)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 206:213)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 214:244)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 245:290)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 291:298)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 299:338)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 339:378)

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