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- PDB-9etl: Mouse CNPase catalytic domain with nanobody 8D -

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Basic information

Entry
Database: PDB / ID: 9etl
TitleMouse CNPase catalytic domain with nanobody 8D
Components
  • 2',3'-cyclic-nucleotide 3'-phosphodiesterase
  • Chains: D,C
KeywordsPROTEIN BINDING / CNPase / myelin / nanobody / single-domain antibody / complex
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
Cyclic nucleotide phosphodiesterase / : / 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase) / Cyclic phosphodiesterase / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSchroder, M. / Markusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: Mouse CNPase catalytic domain with nanobody 8D
Authors: Schroder, M. / Markusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Chains: D,C
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
C: Chains: D,C


Theoretical massNumber of molelcules
Total (without water)75,0854
Polymers75,0854
Non-polymers00
Water6,251347
1
D: Chains: D,C
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)37,5432
Polymers37,5432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
C: Chains: D,C


Theoretical massNumber of molelcules
Total (without water)37,5432
Polymers37,5432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.300, 46.541, 91.976
Angle α, β, γ (deg.)95.657, 100.112, 90.077
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 162 through 218 or resid 220...
d_2ens_1(chain "B" and (resid 162 through 218 or resid 220 through 361 or resid 363 through 378))
d_1ens_2(chain "C" and resid 2 through 122)
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LYSLYSVALVALAB162 - 2184 - 60
d_12ens_1TYRTYRALAALAAB220 - 29662 - 138
d_13ens_1ALAALALEULEUAB298 - 361140 - 203
d_14ens_1LEULEUGLYGLYAB363 - 378205 - 220
d_21ens_1LYSLYSVALVALBC162 - 2184 - 60
d_22ens_1TYRTYRLEULEUBC220 - 36162 - 203
d_23ens_1LEULEUGLYGLYBC363 - 378205 - 220
d_11ens_2VALVALSERSERCD2 - 1222 - 122
d_21ens_2VALVALSERSERDA2 - 1222 - 122

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999976926776, 0.00199388306957, 0.00649386992417), (0.00195127627781, 0.999976573813, -0.00656081895958), (-0.00650679930341, -0.006547996246, -0.999957391746)34.2525418011, 23.1085502587, -50.2306105084
2given(-0.999975323313, -0.00447362529301, -0.00541658955924), (-0.00428368227227, 0.9993925881, -0.0345847497838), (0.00556801866966, -0.034560693398, -0.999387089991)34.0982944565, -24.7939034753, -49.6623547649

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Components

#1: Antibody Chains: D,C


Mass: 13331.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Anti-CNPase nanobody 8D / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein 2',3'-cyclic-nucleotide 3'-phosphodiesterase / CNP / CNPase


Mass: 24210.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Mouse CNPase catalytic domain / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnp, Cnp1 / Production host: Escherichia coli (E. coli)
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M phosphate-citrate pH 4.2, 18% PEG8000, 0.35M NaCl
PH range: 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 190179 / % possible obs: 89.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 25.15 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.091 / Net I/σ(I): 6.9
Reflection shellResolution: 1.5→1.59 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 13946 / CC1/2: 0.224 / Rrim(I) all: 2.368 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→45.05 Å / SU ML: 0.2863 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.7416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 3731 2.08 %
Rwork0.1785 175417 -
obs0.1796 179148 81.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.35 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5077 0 0 347 5424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01065202
X-RAY DIFFRACTIONf_angle_d1.00647017
X-RAY DIFFRACTIONf_chiral_restr0.0811763
X-RAY DIFFRACTIONf_plane_restr0.0092895
X-RAY DIFFRACTIONf_dihedral_angle_d12.97021907
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAX-RAY DIFFRACTIONTorsion NCS0.436573412026
ens_2d_2DCX-RAY DIFFRACTIONTorsion NCS0.28971162691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.3548360.36871775X-RAY DIFFRACTION22.53
1.52-1.540.3604990.36743931X-RAY DIFFRACTION49.29
1.54-1.560.42461130.36095354X-RAY DIFFRACTION66.31
1.56-1.580.39691070.36146066X-RAY DIFFRACTION76.49
1.58-1.610.36451410.35536535X-RAY DIFFRACTION81.34
1.61-1.630.4011360.35256746X-RAY DIFFRACTION84.5
1.63-1.660.4111490.34956825X-RAY DIFFRACTION84.59
1.66-1.690.35611440.33646615X-RAY DIFFRACTION84.72
1.69-1.720.40881370.31296652X-RAY DIFFRACTION83.06
1.72-1.750.39961370.29366334X-RAY DIFFRACTION78.51
1.75-1.790.29561280.26886367X-RAY DIFFRACTION79.83
1.79-1.820.26851710.2497187X-RAY DIFFRACTION90.39
1.82-1.870.28771310.2337241X-RAY DIFFRACTION90.14
1.87-1.910.2711740.21947164X-RAY DIFFRACTION89.88
1.91-1.960.27551470.19987201X-RAY DIFFRACTION89.48
1.96-2.020.29511430.18937196X-RAY DIFFRACTION89.92
2.02-2.090.22141630.16137011X-RAY DIFFRACTION88.15
2.09-2.160.20441380.15047010X-RAY DIFFRACTION88.64
2.16-2.250.23411530.14357000X-RAY DIFFRACTION86.31
2.25-2.350.20591380.15216675X-RAY DIFFRACTION83.78
2.35-2.480.23291300.14996083X-RAY DIFFRACTION75.95
2.48-2.630.27661630.16597196X-RAY DIFFRACTION90.58
2.63-2.830.18531490.15157189X-RAY DIFFRACTION90.19
2.83-3.120.24641550.16457223X-RAY DIFFRACTION90.48
3.12-3.570.18591550.14587154X-RAY DIFFRACTION89.07
3.57-4.50.15921430.14626582X-RAY DIFFRACTION82.98
4.5-45.050.21991510.17567105X-RAY DIFFRACTION88.7

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