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

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Basic information

Entry
Database: PDB / ID: 3zbz
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 / oligodendrocyte differentiation / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / extracellular space ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / oligodendrocyte differentiation / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / 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
ACETIC ACID / 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: 2.1 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 14, 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)24,6893
Polymers24,2661
Non-polymers4232
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.250, 46.990, 107.380
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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#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.: 117 / 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 2 (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 WITH 10 MM 23-RP-CYCLIC AMPS WAS MIXED IN 0.5 PLUS 0.5 UL DROPS WITH 30% 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 SX-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: 2.1→30 Å / Num. obs: 12529 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 24.33 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 93

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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: 2.1→28.474 Å / SU ML: 0.23 / σ(F): 2.01 / Phase error: 24.87 / Stereochemistry target values: ML
Details: HYDROGENS WERE INCLUDED IN RIDING POSITION. RESIDUES 158-162, 209-213, AND 293-295 WERE EXCLUDED FROM MODEL DUE TO INSUFFICIENT ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2646 625 5 %
Rwork0.2075 --
obs0.2104 12495 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 27 117 1754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021694
X-RAY DIFFRACTIONf_angle_d0.5942287
X-RAY DIFFRACTIONf_dihedral_angle_d11.701620
X-RAY DIFFRACTIONf_chiral_restr0.037247
X-RAY DIFFRACTIONf_plane_restr0.003287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.31120.30241470.2482810X-RAY DIFFRACTION95
2.3112-2.64540.27451540.2372915X-RAY DIFFRACTION98
2.6454-3.33210.28291570.21462987X-RAY DIFFRACTION99
3.3321-28.47630.23961670.18343158X-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)
13.4156-0.94751.84713.4562-1.23613.1208-0.01510.0504-0.17210.40590.0466-0.19460.1820.3437-0.05730.2062-0.0036-0.02860.3119-0.040.16185.13624.426-15.5364
20.08880.51180.223.1674-0.8433.89650.1904-0.3048-0.1722-0.483-0.0741-0.02960.04680.6956-0.120.20780.02320.0030.1819-0.01070.2347-0.64527.5984-22.6943
31.86370.18830.05312.7783-0.23212.063-0.0807-0.03130.06020.28350.05770.6046-0.1913-0.22470.04860.1580.00420.02380.2011-0.03280.2428-11.51113.5189-19.3509
41.80541.6217-0.89042.06990.49792.9280.2092-1.4103-1.75460.75780.22011.74121.2692-0.7791-0.05220.5668-0.1160.28840.44110.25550.7031-16.60565.5485-12.3563
55.2387-1.3177-0.39055.10290.70623.4432-0.0354-0.209-0.39930.5446-0.19050.36960.3409-0.03940.21670.2403-0.0022-0.03420.1912-0.00250.1952-5.17880.2404-14.2074
62.5908-0.33961.04131.9555-1.09482.7257-0.0419-0.4750.13620.947-0.1411-0.0419-0.38090.02480.12710.467-0.0436-0.0420.3138-0.02670.19370.56817.8858-7.3719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 163 THROUGH 220 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 221 THROUGH 235 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 236 THROUGH 288 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 289 THROUGH 308 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 309 THROUGH 336 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 337 THROUGH 378 )

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