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- PDB-2y3x: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -

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Basic information

Entry
Database: PDB / ID: 2y3x
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, complexed with sulfate
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 / 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
2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJan 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,02715
Polymers72,8823
Non-polymers1,14512
Water2,864159
1
A: 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7746
Polymers24,2941
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9588
Polymers24,2941
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE


Theoretical massNumber of molelcules
Total (without water)24,2941
Polymers24,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.430, 82.430, 86.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A165 - 379
2114E165 - 379

NCS oper: (Code: given
Matrix: (-0.9998, -0.01424, 0.01338), (-0.01466, 0.9994, -0.03127), (-0.01292, -0.03146, -0.9994)
Vector: 41.29, 24.26, -19.44)

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Components

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


Mass: 24293.928 Da / Num. of mol.: 3 / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 3.5
Details: 50MM NA-CITRATE PH 3.5, 2.9M AMMONIUM SULFATE, 10% PEG 550 MME

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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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.788
11-H, H+K, -L20.212
ReflectionResolution: 2.1→35 Å / Num. obs: 38236 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.85 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.98
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.83 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMI

2xmi


Resolution: 2.1→71.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.021 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1981 5.2 %RANDOM
Rwork0.18971 ---
obs0.19162 36254 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 71.987 Å2
Baniso -1Baniso -2Baniso -3
1-30.58 Å20 Å20 Å2
2--30.58 Å20 Å2
3----61.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→71.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 62 159 5198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225140
X-RAY DIFFRACTIONr_bond_other_d0.0050.023601
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.9946927
X-RAY DIFFRACTIONr_angle_other_deg1.09738802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.38724.059202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34915913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3791521
X-RAY DIFFRACTIONr_chiral_restr0.1250.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
X-RAY DIFFRACTIONr_nbd_refined0.2120.21067
X-RAY DIFFRACTIONr_nbd_other0.1840.23281
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22479
X-RAY DIFFRACTIONr_nbtor_other0.0880.22614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1030.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.256
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.66823161
X-RAY DIFFRACTIONr_mcbond_other0.48121314
X-RAY DIFFRACTIONr_mcangle_it2.60935039
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.39141979
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.70551888
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2792 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.060.05
2Emedium positional0.060.05
1Amedium thermal24.76
2Emedium thermal24.76
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 103 -
Rwork0.193 2690 -
obs--99.08 %
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)
13.0158-0.109-1.02412.08220.38651.7983-0.4023-0.0216-0.0538-0.05950.5139-0.0108-0.0659-0.0504-0.11160.01890.0206-0.01810.37410.01040.49852.056314.3114-12.0103
21.7156-0.76570.93512.1254-0.86612.2340.0047-0.0088-0.02210.04050.00680.04430.0666-0.2565-0.01160.0869-0.02740.04320.14130.00410.472929.480715.438918.7491
35.09750.5009-4.60123.474-0.45443.46610.23680.38790.7585-0.21780.08830.0143-0.3456-0.3666-0.32520.34-0.1616-0.39860.78710.01890.638738.6939-9.8616-7.7842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A164 - 378
2X-RAY DIFFRACTION2B160 - 378
3X-RAY DIFFRACTION3E164 - 378

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