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

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Basic information

Entry
Database: PDB / ID: 3zbr
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H230S, crystallized with 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 / 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
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: 2.304 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
B: 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9734
Polymers48,4862
Non-polymers1,4872
Water1,58588
1
A: 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9862
Polymers24,2431
Non-polymers7431
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)24,9862
Polymers24,2431
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.100, 47.100, 111.170
Angle α, β, γ (deg.)90.00, 90.26, 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: 24242.857 Da / Num. of mol.: 2 / 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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). HISTIDINE 230 IS MUTATED TO SERINE.

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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: 2.2 Å3/Da / Density % sol: 44.8 % / Description: NONE
Crystal growTemperature: 277 K / pH: 4
Details: 250 UM PROTEIN WITH 10 MM 23-CNADP MIXED IN 0.5 PLUS 0.5 UL DROPS WITH 50 MM NA-FORMATE (1:2 PH3:PH5) AND 23% PEG 4000 IN 4 DEGC

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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: Feb 2, 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
Reflection twinOperator: h,-k,-l / Fraction: 0.46
ReflectionResolution: 2.3→30 Å / Num. obs: 19310 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 44.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.3 / % possible all: 91.2

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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: 2.304→29.123 Å / σ(F): 1.99 / Phase error: 27.5 / Stereochemistry target values: TWIN_LSQ_F
Details: HYDROGENS WERE INCLUDED IN RIDING POSITIONS. RESIDUES 158-160, 210-212 FROM CHAIN A, AND RESIDUES 158-160, 210-213 AND 294-296 WERE EXCLUDED FROM THE MODEL DUE TO INSUFFICIENT ELECTRON DENSITY
RfactorNum. reflection% reflection
Rfree0.2612 974 5.1 %
Rwork0.2202 --
obs0.2264 19304 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.5 Å2
Refinement stepCycle: LAST / Resolution: 2.304→29.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 96 88 3487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033477
X-RAY DIFFRACTIONf_angle_d0.9884699
X-RAY DIFFRACTIONf_dihedral_angle_d18.4181297
X-RAY DIFFRACTIONf_chiral_restr0.047508
X-RAY DIFFRACTIONf_plane_restr0.004582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3056-2.42710.38591330.31012526X-RAY DIFFRACTION91
2.4271-2.57910.35641360.27832581X-RAY DIFFRACTION94
2.5791-2.77810.29391380.26372616X-RAY DIFFRACTION94
2.7781-3.05730.33181370.24262609X-RAY DIFFRACTION95
3.0573-3.4990.24871400.22632662X-RAY DIFFRACTION95
3.499-4.40550.23731390.20012622X-RAY DIFFRACTION94
4.4055-27.88110.21911430.18812713X-RAY DIFFRACTION94
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)
120.3784-0.36262.7129-0.62741.9203-0.0645-0.02850.058-0.32520.0465-0.4328-0.05740.3066-0.03880.2312-0.03250.00040.1674-0.05210.164566.3829-6.441745.0522
21.45310.8545-0.59941.4728-0.60461.6101-0.04020.32020.0661-0.2230.08810.1970.0257-0.0346-0.06170.26480.0348-0.06990.234-0.01010.152255.8573-9.900543.6506
32.3797-0.54170.31772.0659-0.30631.9634-0.0115-0.001-0.0992-0.1090.1045-0.20680.23660.4208-0.06630.2209-0.0003-0.05950.3261-0.04780.450745.5912-22.894910.5457
41.7548-0.56360.63251.4638-0.87412.0474-0.0002-0.3624-0.0298-0.04720.08610.11880.0003-0.054-0.10620.15970.03070.00590.26890.00770.445535.7578-19.618311.95
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 161 THROUGH 216)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 217 THROUGH 378)
3X-RAY DIFFRACTION3CHAIN B AND (RESID 161 THROUGH 216)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 217 THROUGH 378)

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