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- PDB-5aan: Crystal structure of Drosophila NCS-1 bound to penothiazine FD44 -

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Basic information

Entry
Database: PDB / ID: 5aan
TitleCrystal structure of Drosophila NCS-1 bound to penothiazine FD44
ComponentsCG5907-PA, ISOFORM A
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
N-phenothiazin-10-yl-2-piperidin-1-yl-ethanamide / Frequenin-2
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChaves-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
DepositionJul 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Mar 8, 2017Group: Other
Revision 1.3Dec 27, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jan 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CG5907-PA, ISOFORM A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5026
Polymers21,9221
Non-polymers5805
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.052, 54.961, 61.132
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 CG5907-PA, ISOFORM A / FREQUENIN 2


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) / Plasmid: PETDUET-1 / 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-XOC / N-phenothiazin-10-yl-2-piperidin-1-yl-ethanamide / FD44


Mass: 339.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3OS
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 7.5, 70% V/V 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2015 / Details: SI ELLIPTICALLY BENT MIRROR
RadiationMonochromator: SI(111) CHANNEL-CUT, CRYOCOOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 24712 / % possible obs: 100 % / Observed criterion σ(I): 1.2 / Redundancy: 12.2 % / Biso Wilson estimate: 27.32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.9
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.2 / % possible all: 100

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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
Resolution: 1.6→40.871 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1246 5.1 %
Rwork0.1855 --
obs0.1868 24656 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→40.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 35 146 1699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141645
X-RAY DIFFRACTIONf_angle_d1.2422192
X-RAY DIFFRACTIONf_dihedral_angle_d13.908650
X-RAY DIFFRACTIONf_chiral_restr0.061223
X-RAY DIFFRACTIONf_plane_restr0.006292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.66410.30461090.29872586X-RAY DIFFRACTION100
1.6641-1.73990.32341430.26652557X-RAY DIFFRACTION100
1.7399-1.83160.27351320.23112568X-RAY DIFFRACTION100
1.8316-1.94640.29931280.21542561X-RAY DIFFRACTION100
1.9464-2.09660.23121420.19372589X-RAY DIFFRACTION100
2.0966-2.30760.23571170.182589X-RAY DIFFRACTION100
2.3076-2.64150.20111640.17712585X-RAY DIFFRACTION100
2.6415-3.32770.19981500.18062624X-RAY DIFFRACTION100
3.3277-40.88470.1851610.17252751X-RAY DIFFRACTION100

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