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

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Basic information

Entry
Database: PDB / ID: 3zbs
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation V321A, crystallized with 2'-AMPS
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'-O-(sulfidophosphinato)adenosine / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMyllykoski, M. / Raasakka, A. / Lehtimaki, M. / Han, H. / Kursula, P.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystallographic Analysis of the Reaction Cycle of 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family
Authors: Myllykoski, M. / Raasakka, A. / Lehtimaki, M. / Han, H. / Kursula, I. / Kursula, P.
History
DepositionNov 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6653
Polymers24,2661
Non-polymers3992
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.360, 46.880, 107.230
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 / CNP / CNPASE


Mass: 24265.875 Da / Num. of mol.: 1 / Fragment: C-TERMINAL CATALYTIC DOMAIN, RESIDUES 159-378 / Mutation: YES
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): BL21(DE3) / 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: Chemical ChemComp-OVE / 2'-O-(sulfidophosphinato)adenosine / ADENOSINE-2'-MONOPHOSPHOROTHIOATE


Mass: 363.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL GLYCINE REMAINS FROM TEV-CLEAVAGE OF EXPRESSION TAG. RESIDUE NUMBERING IS ACCORDING TO ...N-TERMINAL GLYCINE REMAINS FROM TEV-CLEAVAGE OF EXPRESSION TAG. RESIDUE NUMBERING IS ACCORDING TO CNPASE ISOFORM 1 ( P16330-2). VALINE 321 IS MUTATED TO ALANINE.

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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: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE
Crystal growTemperature: 277 K / pH: 4
Details: 250 UM PROTEIN AND 10 MM 23-SP-CAMPS WERE MIXED IN 0.5 PLUS 0.5 UL DROPS WITH 25% PEG4000 AND 50 MM ACETATE PH 3 IN 4 DEG C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04088
DetectorType: MARRESEARCH MX-165 / Detector: CCD / Date: Mar 1, 2012
Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M)
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04088 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 8049 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 31.56 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.2
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 6 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.2 / % possible all: 97.6

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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 2XMI

2xmi


Resolution: 2.45→28.424 Å / SU ML: 0.25 / σ(F): 2 / Phase error: 22.29 / Stereochemistry target values: ML
Details: HYDROGENS WERE ADDED IN RIDING POSITION. RESIDUES 158-162, 209-212, AND 293-295 WERE EXCLUDED FROM MODEL DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2415 403 5 %
Rwork0.1838 --
obs0.1866 8048 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.9 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 24 85 1728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021719
X-RAY DIFFRACTIONf_angle_d0.5722324
X-RAY DIFFRACTIONf_dihedral_angle_d9.674638
X-RAY DIFFRACTIONf_chiral_restr0.035250
X-RAY DIFFRACTIONf_plane_restr0.002293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.80440.28031300.22192464X-RAY DIFFRACTION99
2.8044-3.53220.25021330.19472524X-RAY DIFFRACTION99
3.5322-28.42590.22381400.16482657X-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)
11.34610.39920.34022.496-0.59182.02920.00890.16460.18680.2629-0.1249-0.40590.07930.39990.07620.1726-0.012-0.01360.1977-0.02560.19463.93587.1789-16.1248
21.7524-0.7120.67142.3375-0.43231.6969-0.0169-0.1289-0.14490.1610.07090.32290.01990.0005-0.01860.15-0.02740.03070.1146-0.00130.1232-6.09349.0798-19.205
32.5651-1.2445-1.1720.74560.80970.9542-0.1077-0.0467-0.66140.57310.0030.63190.154-0.11270.29260.29270.07910.13180.23380.05950.3438-9.79773.3998-16.0221
41.2827-0.50350.93161.3348-0.42231.1345-0.1355-0.25530.09290.68460.01390.0039-0.0997-0.12120.1160.36180.01910.00160.2018-0.02930.153-1.5916.1499-7.4785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 163 THROUGH 204 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 205 THROUGH 288 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 289 THROUGH 321 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 322 THROUGH 378 )

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