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- PDB-5fyx: Crystal structure of Drosophila NCS-1 bound to penothiazine FD16 -

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Basic information

Entry
Database: PDB / ID: 5fyx
TitleCrystal structure of Drosophila NCS-1 bound to penothiazine FD16
ComponentsFREQUENIN 2Neuronal calcium sensor-1
KeywordsCALCIUM-BINDING PROTEIN / CALCIUM SENSOR
Function / homology
Function and homology information


calcium sensitive guanylate cyclase activator activity / regulation of neurotransmitter secretion / neurotransmitter secretion / neuromuscular junction development / vesicle-mediated transport / synaptic vesicle / chemical synaptic transmission / calcium ion binding / cytoplasm
Similarity search - Function
Recoverin family / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...Recoverin family / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FD6 / Frequenin-2
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMartinez-Gonzalez, L. / Chaves-Sanjuan, A. / Infantes, L. / Sanchez-Barrena, M.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Interference of the complex between NCS-1 and Ric8a with phenothiazines regulates synaptic function and is an approach for fragile X syndrome.
Authors: Mansilla, A. / Chaves-Sanjuan, A. / Campillo, N.E. / Semelidou, O. / Martinez-Gonzalez, L. / Infantes, L. / Gonzalez-Rubio, J.M. / Gil, C. / Conde, S. / Skoulakis, E.M. / Ferrus, A. / ...Authors: Mansilla, A. / Chaves-Sanjuan, A. / Campillo, N.E. / Semelidou, O. / Martinez-Gonzalez, L. / Infantes, L. / Gonzalez-Rubio, J.M. / Gil, C. / Conde, S. / Skoulakis, E.M. / Ferrus, A. / Martinez, A. / Sanchez-Barrena, M.J.
History
DepositionMar 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Dec 27, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: FREQUENIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,12711
Polymers21,9221
Non-polymers1,20410
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.057, 62.997, 63.425
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 FREQUENIN 2 / Neuronal calcium sensor-1


Mass: 21922.443 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VWX8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-FD6 / N-[2-(2-chloranylphenothiazin-10-yl)ethyl]-4-methyl-piperazin-1-amine / FD16


Mass: 374.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23ClN4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsI178M MUTATION

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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: 2.47 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growDetails: 54% W/V MPD, 0.1M TRIS PH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979236
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979236 Å / Relative weight: 1
ReflectionResolution: 1.8→44.7 Å / Num. obs: 20513 / % possible obs: 99.4 % / Observed criterion σ(I): 0.5 / Redundancy: 13 % / Biso Wilson estimate: 36.74 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 0.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BY4

4by4


Resolution: 1.8→44.696 Å / SU ML: 0.33 / σ(F): 0.4 / Phase error: 34.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1842 4.8 %
Rwork0.2283 --
obs0.2294 20464 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 76 82 1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041537
X-RAY DIFFRACTIONf_angle_d0.872077
X-RAY DIFFRACTIONf_dihedral_angle_d18.109607
X-RAY DIFFRACTIONf_chiral_restr0.043212
X-RAY DIFFRACTIONf_plane_restr0.004264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.59361260.47042796X-RAY DIFFRACTION99
1.8487-1.90310.51721220.43132822X-RAY DIFFRACTION98
1.9031-1.96450.46051400.40572798X-RAY DIFFRACTION99
1.9645-2.03470.37871830.35692762X-RAY DIFFRACTION99
2.0347-2.11620.28791520.32832795X-RAY DIFFRACTION99
2.1162-2.21250.37611420.29382797X-RAY DIFFRACTION99
2.2125-2.32920.3181670.29332812X-RAY DIFFRACTION99
2.3292-2.47510.28031720.26822787X-RAY DIFFRACTION99
2.4751-2.66620.26761280.24642838X-RAY DIFFRACTION100
2.6662-2.93440.2722840.2562857X-RAY DIFFRACTION99
2.9344-3.35890.26261320.22172885X-RAY DIFFRACTION100
3.3589-4.23140.20711740.18162796X-RAY DIFFRACTION100
4.2314-44.70990.19711200.17952858X-RAY DIFFRACTION100

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