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- PDB-4yru: Crystal structure of C-terminally truncated Neuronal Calcium Sens... -

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Basic information

Entry
Database: PDB / ID: 4yru
TitleCrystal structure of C-terminally truncated Neuronal Calcium Sensor (NCS-1) from Rattus norvegicus
ComponentsNeuronal calcium sensor 1
KeywordsSIGNALING PROTEIN / EF-hand / Calcium sensor / C-terminal truncation
Function / homology
Function and homology information


calcium-dependent protein kinase inhibitor activity / calcium sensitive guanylate cyclase activator activity / regulation of presynaptic cytosolic calcium ion concentration / dense core granule / regulation of neuron projection development / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / regulation of signal transduction / postsynaptic cytosol / voltage-gated calcium channel activity ...calcium-dependent protein kinase inhibitor activity / calcium sensitive guanylate cyclase activator activity / regulation of presynaptic cytosolic calcium ion concentration / dense core granule / regulation of neuron projection development / regulation of synaptic vesicle exocytosis / positive regulation of exocytosis / regulation of signal transduction / postsynaptic cytosol / voltage-gated calcium channel activity / presynaptic cytosol / positive regulation of calcium-mediated signaling / calyx of Held / postsynapse / postsynaptic density / axon / dendrite / calcium ion binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / Golgi apparatus / plasma membrane / cytoplasm
Similarity search - Function
Recoverin family / EF hand domain / 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 domain / 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
Neuronal calcium sensor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPandalaneni, S. / Karrupiah, V. / Mayans, O. / Derrick, J.P. / Lian, L.Y.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Neuronal Calcium Sensor-1 Binds the D2 Dopamine Receptor and G-protein-coupled Receptor Kinase 1 (GRK1) Peptides Using Different Modes of Interactions.
Authors: Pandalaneni, S. / Karuppiah, V. / Saleem, M. / Haynes, L.P. / Burgoyne, R.D. / Mayans, O. / Derrick, J.P. / Lian, L.Y.
History
DepositionMar 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuronal calcium sensor 1
B: Neuronal calcium sensor 1
C: Neuronal calcium sensor 1
D: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,65316
Polymers82,1724
Non-polymers48112
Water28816
1
A: Neuronal calcium sensor 1
D: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3278
Polymers41,0862
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-82 kcal/mol
Surface area15790 Å2
MethodPISA
2
B: Neuronal calcium sensor 1
C: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3278
Polymers41,0862
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-79 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.680, 88.800, 100.670
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
Neuronal calcium sensor 1 / NCS-1 / Frequenin homolog / Frequenin-like protein / Frequenin-like ubiquitous protein


Mass: 20543.092 Da / Num. of mol.: 4 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ncs1, Flup, Freq / Production host: Escherichia coli (E. coli) / References: UniProt: P62168
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES pH6.0, 200mM NaCl,16% (w/v) PEG 6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→66.59 Å / Num. obs: 16258 / % possible obs: 98 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 1.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.374 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2you

2you
PDB Unreleased entry


Resolution: 2.8→66.59 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2909 488 3.01 %
Rwork0.2467 --
obs0.2481 16212 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→66.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 12 16 5214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035296
X-RAY DIFFRACTIONf_angle_d0.7477125
X-RAY DIFFRACTIONf_dihedral_angle_d11.7931961
X-RAY DIFFRACTIONf_chiral_restr0.03752
X-RAY DIFFRACTIONf_plane_restr0.003927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.20520.3381600.29975140X-RAY DIFFRACTION98
3.2052-4.03810.30731600.25225183X-RAY DIFFRACTION97
4.0381-66.61310.26091680.22195401X-RAY DIFFRACTION98
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)
12.3505-0.0981.05661.45631.23145.0723-0.0014-0.3677-0.26430.19420.0430.05440.2859-0.0797-0.01730.3033-0.0638-0.00970.67070.04880.11435.7912-2.0745-5.1012
21.57930.00460.28711.6035-1.22432.4783-0.1130.00330.0202-0.0795-0.0585-0.30430.01960.19450.17910.2816-0.07630.03190.75130.03510.1357-5.7814-2.885230.9494
30.83880.4194-0.38391.5288-0.99982.0957-0.0456-0.04910.16470.1120.07560.23140.0580.0403-0.18420.31750.02460.04130.7180.05630.0899-23.32638.269919.9467
40.4153-0.0403-0.00840.85410.12443.247-0.0064-0.1944-0.07670.161-0.0165-0.12570.01680.1857-0.0090.281-0.0139-0.01970.7125-0.08370.048822.88067.6626.2334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 16 through 174)
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 175)
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 174)
4X-RAY DIFFRACTION4(chain 'D' and resid 8 through 173)

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