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- PDB-9ert: Mouse CNPase catalytic domain with nano body 5E -

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Basic information

Entry
Database: PDB / ID: 9ert
TitleMouse CNPase catalytic domain with nano body 5E
Components
  • 2',3'-cyclic-nucleotide 3'-phosphodiesterase
  • Chains: B
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 / 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
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
PHOSPHATE ION / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMarkusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mouse CNPase catalytic domain with nano body 5E
Authors: Markusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.
History
DepositionMar 25, 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
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
B: Chains: B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5083
Polymers38,4132
Non-polymers951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.832, 110.832, 83.281
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein 2',3'-cyclic-nucleotide 3'-phosphodiesterase / CNP / CNPase


Mass: 24236.875 Da / Num. of mol.: 1
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
#2: Antibody Chains: B


Mass: 14176.308 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Anti-CNPase nanobody 5E / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN
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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Na/K phosphate pH 7.0, 25% PEG3350

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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: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 10986 / % possible obs: 70 % / Redundancy: 5.6 % / Biso Wilson estimate: 68.32 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.142 / Net I/σ(I): 10.3
Reflection shellResolution: 2.75→3.15 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 918 / CC1/2: 0.58 / Rrim(I) all: 1.363 / % possible all: 18

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→47.99 Å / SU ML: 0.4728 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.8908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3232 1105 10.09 %
Rwork0.2894 9844 -
obs0.2929 10949 69.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.19 Å2
Refinement stepCycle: LAST / Resolution: 2.75→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 5 0 2641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242699
X-RAY DIFFRACTIONf_angle_d0.55853646
X-RAY DIFFRACTIONf_chiral_restr0.0375387
X-RAY DIFFRACTIONf_plane_restr0.0051471
X-RAY DIFFRACTIONf_dihedral_angle_d16.7083970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.880.3748100.3908101X-RAY DIFFRACTION5.8
2.88-3.030.5153330.3704305X-RAY DIFFRACTION17.67
3.03-3.220.4144830.3651732X-RAY DIFFRACTION42.12
3.22-3.470.37421810.30841625X-RAY DIFFRACTION92.71
3.47-3.810.31061910.31581720X-RAY DIFFRACTION99.43
3.82-4.370.3361990.2531766X-RAY DIFFRACTION99.9
4.37-5.50.29391980.27511767X-RAY DIFFRACTION99.9
5.5-47.990.31112100.29281828X-RAY DIFFRACTION98.74
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)
10.4497083634180.04662819421070.2701501368630.210802731692-0.0317282933120.2257435809460.1231085169670.4979846830440.178064536651-0.380967775962-0.1267760581280.269325162947-0.160831440639-0.0752852574713-0.1392487936960.2997458170230.3820738040890.01092810588360.6277012433250.1106572995640.424344399889-9.2299626170478.0895608235.5161627945
20.0950143690580.09845968283110.0116839527090.1763030614870.01943690529510.09436544148560.0717685017374-0.0781775577733-0.03012968579730.109531243397-0.0165044855826-0.100390240944-0.024017738636-0.1236968384840.153222431594-0.02332983704530.3454409383140.2363206297830.262459686448-0.138098988410.087866351940318.012068511958.561374226538.2298554439
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 163 through 378)AA163 - 3781 - 210
22(chain 'B' and resid 1 through 132)BB1 - 1321 - 132

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