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- PDB-5ae0: Perdeuterated mouse CNPase catalytic domain at atomic resolution -

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Basic information

Entry
Database: PDB / ID: 5ae0
TitlePerdeuterated mouse CNPase catalytic domain at atomic resolution
Components2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
KeywordsHYDROLASE
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
CITRIC ACID / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsLaulumaa, S. / 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
DepositionAug 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / exptl_crystal_grow
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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method
Revision 2.1Jan 10, 2024Group: 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)24,5223
Polymers24,2941
Non-polymers2282
Water5,080282
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.650, 47.560, 51.220
Angle α, β, γ (deg.)90.00, 97.51, 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, UNP RESIDUES 179-398
Source method: isolated from a genetically manipulated source
Details: PERDEUTERATED / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETNKI-HIS3C-LIC-KAN / 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 282 / 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: 1.97 Å3/Da / Density % sol: 37.59 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 3.5 / Details: 25% PEG3350, 50 MM ACETATE, PD 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.913
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 1.04→30 Å / Num. obs: 90347 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 8.77 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 1.04→1.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 1.1 / % possible all: 99.1

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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 2WUT

2wut


Resolution: 1.04→29.287 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 17.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1563 1807 2 %
Rwork0.127 --
obs0.1276 90320 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.04→29.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 14 282 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192200
X-RAY DIFFRACTIONf_angle_d1.6183028
X-RAY DIFFRACTIONf_dihedral_angle_d16.639854
X-RAY DIFFRACTIONf_chiral_restr0.384307
X-RAY DIFFRACTIONf_plane_restr0.011414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.06810.31941370.28946730X-RAY DIFFRACTION99
1.0681-1.09950.27371380.24486743X-RAY DIFFRACTION99
1.0995-1.1350.24191380.20196758X-RAY DIFFRACTION100
1.135-1.17560.22251380.16416780X-RAY DIFFRACTION100
1.1756-1.22270.17671390.14586802X-RAY DIFFRACTION100
1.2227-1.27830.17461390.13446807X-RAY DIFFRACTION100
1.2783-1.34570.16231390.12016812X-RAY DIFFRACTION100
1.3457-1.430.16291390.10816803X-RAY DIFFRACTION100
1.43-1.54040.15821390.09346806X-RAY DIFFRACTION100
1.5404-1.69540.11661380.08016805X-RAY DIFFRACTION100
1.6954-1.94070.11571400.08646849X-RAY DIFFRACTION100
1.9407-2.44490.11111400.10686853X-RAY DIFFRACTION100
2.4449-29.2990.15221430.12846965X-RAY DIFFRACTION100

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