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- PDB-9eru: Mouse CNPase catalytic domain with nanobody 7E -

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Basic information

Entry
Database: PDB / ID: 9eru
TitleMouse CNPase catalytic domain with nanobody 7E
Components
  • 2',3'-cyclic-nucleotide 3'-phosphodiesterase
  • Chains: G,C,E,H
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
2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 nanobody 7E
Authors: Markusson, S. / Raasakka, A. / Opazo, F. / Kursula, P.
History
DepositionMar 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,4218
Polymers152,4218
Non-polymers00
Water543
1
B: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
G: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-9 kcal/mol
Surface area15800 Å2
MethodPISA
2
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
C: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-10 kcal/mol
Surface area15730 Å2
MethodPISA
3
D: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
E: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-9 kcal/mol
Surface area15410 Å2
MethodPISA
4
F: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
H: Chains: G,C,E,H


Theoretical massNumber of molelcules
Total (without water)38,1052
Polymers38,1052
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-8 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.150, 79.000, 117.590
Angle α, β, γ (deg.)77.675, 87.706, 84.290
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 24236.875 Da / Num. of mol.: 4
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: G,C,E,H


Mass: 13868.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Anti-CNPase nanobody 7E / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M MIB pH 4.0, 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: 2.5→50 Å / Num. obs: 41229 / % possible obs: 91.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 54.93 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.205 / Net I/σ(I): 5.5
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3026 / CC1/2: 0.335 / Rrim(I) all: 2.914 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→41.96 Å / SU ML: 0.5228 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.4522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3004 1994 4.85 %
Rwork0.2545 39151 -
obs0.2567 41145 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10333 0 0 3 10336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004110559
X-RAY DIFFRACTIONf_angle_d0.664814271
X-RAY DIFFRACTIONf_chiral_restr0.04351551
X-RAY DIFFRACTIONf_plane_restr0.0041819
X-RAY DIFFRACTIONf_dihedral_angle_d13.52163829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.46391420.45232764X-RAY DIFFRACTION90.87
2.56-2.630.45021380.41382697X-RAY DIFFRACTION87.2
2.63-2.710.39551270.39452513X-RAY DIFFRACTION83.02
2.71-2.80.41481450.3662899X-RAY DIFFRACTION95.1
2.8-2.90.3941490.36262914X-RAY DIFFRACTION94.68
2.9-3.010.41521480.36142903X-RAY DIFFRACTION95.49
3.01-3.150.35291450.32752858X-RAY DIFFRACTION93.79
3.15-3.320.38411470.29292882X-RAY DIFFRACTION93.81
3.32-3.520.29111420.26692776X-RAY DIFFRACTION91.65
3.52-3.790.2941390.24682731X-RAY DIFFRACTION88.33
3.8-4.180.26931380.21612689X-RAY DIFFRACTION87.99
4.18-4.780.21941470.18592897X-RAY DIFFRACTION96.06
4.78-6.020.23271490.20462903X-RAY DIFFRACTION94.28
6.02-41.960.26741380.19922725X-RAY DIFFRACTION89.38

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