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

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Basic information

Entry
Database: PDB / ID: 2ydb
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, soaked with 2',3'-cyclic NADP
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionMar 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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)25,0372
Polymers24,2941
Non-polymers7431
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.740, 46.810, 106.880
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: 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE (NAP): NADP IS ONLY PARTIALLY VISIBLE

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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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 3.5
Details: CRYSTALLIZATION: 50 MM NA-CITRATE PH 3.5 & 30 % PEG 3000, SOAKING: 50 MM NA-CITRATE PH 3.5, 35 % PEG 1500 & 100 MM 2,3-CYCLIC NADP FOR 25 MIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: May 14, 2010
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: 1.03796 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. obs: 11501 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 35.61 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.17
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / % possible all: 90.2

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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: 2.15→23.452 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 574 5 %
Rwork0.1974 --
obs0.2004 11499 96.25 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.098 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso mean: 49.99 Å2
Baniso -1Baniso -2Baniso -3
1-10.5771 Å2-0 Å2-0 Å2
2---7.2356 Å20 Å2
3----3.3415 Å2
Refinement stepCycle: LAST / Resolution: 2.15→23.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 27 60 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061746
X-RAY DIFFRACTIONf_angle_d0.9982360
X-RAY DIFFRACTIONf_dihedral_angle_d18.386652
X-RAY DIFFRACTIONf_chiral_restr0.069254
X-RAY DIFFRACTIONf_plane_restr0.005296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.36630.33061350.26632565X-RAY DIFFRACTION93
2.3663-2.70830.34771430.24922735X-RAY DIFFRACTION98
2.7083-3.41040.26281470.19072786X-RAY DIFFRACTION99
3.4104-23.45320.21811490.17442839X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -3.9799 Å / Origin y: 7.0768 Å / Origin z: -15.3398 Å
111213212223313233
T0.238 Å20.0306 Å20.0126 Å2-0.1845 Å2-0.004 Å2--0.1657 Å2
L0.6532 °2-0.0753 °20.2353 °2-1.9018 °20.0059 °2--0.6644 °2
S-0.0486 Å °-0.0657 Å °0.0738 Å °0.4657 Å °0.102 Å °0.1101 Å °0.0894 Å °-0.0392 Å °-0.0053 Å °
Refinement TLS groupSelection details: ALL

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