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- PDB-4ov2: Crystal structure of C-terminally truncated Neuronal Calcium Sens... -

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Basic information

Entry
Database: PDB / ID: 4ov2
TitleCrystal structure of C-terminally truncated Neuronal Calcium Sensor (NCS-1) from Rattus norvegicus
ComponentsNeuronal calcium sensor 1
KeywordsCALCIUM BINDING PROTEIN
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 / calcium ion binding / dendrite / 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: 2.6 Å
AuthorsPandaleneni, S. / Burgoyne, R. / Mayans, O. / Lian, L.-Y.
CitationJournal: To be Published
Title: Crystal structure of C-terminally truncated Neuronal Calcium Sensor (NCS-1) from Rattus norvegicus
Authors: Pandaleneni, S. / Burgoyne, R. / Mayans, O. / Lian, L.-Y.
History
DepositionFeb 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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_ref_seq_dif.details / _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: 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)83,16616
Polymers82,6854
Non-polymers48112
Water84747
1
A: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7914
Polymers20,6711
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7914
Polymers20,6711
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7914
Polymers20,6711
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7914
Polymers20,6711
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Neuronal calcium sensor 1
D: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5838
Polymers41,3422
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-84 kcal/mol
Surface area15770 Å2
MethodPISA
6
B: Neuronal calcium sensor 1
C: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5838
Polymers41,3422
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-92 kcal/mol
Surface area16340 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: 20671.223 Da / Num. of mol.: 4 / Fragment: C-terminal truncation (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.: 47 / 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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M sodium chloride, 0.1 M MES, pH 6.0, 16% w/v PEG6000, VAPOR DIFFUSION, SITTING DROP

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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: 2.6→66.594 Å / Num. obs: 20185 / % possible obs: 98.8 % / Redundancy: 3 % / Rsym value: 0.2 / Net I/σ(I): 2.3
Reflection shellResolution: 2.6→2.77 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.619 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YOU

2you
PDB Unreleased entry


Resolution: 2.6→66.594 Å / SU ML: 0.52 / σ(F): 1.37 / Phase error: 38.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3082 607 3.01 %
Rwork0.2199 --
obs0.2226 20185 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→66.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 12 47 5245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015296
X-RAY DIFFRACTIONf_angle_d1.2927125
X-RAY DIFFRACTIONf_dihedral_angle_d13.991961
X-RAY DIFFRACTIONf_chiral_restr0.057752
X-RAY DIFFRACTIONf_plane_restr0.008927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.86170.41931490.2994811X-RAY DIFFRACTION98
2.8617-3.27580.34861500.26034848X-RAY DIFFRACTION98
3.2758-4.12710.29441510.20644846X-RAY DIFFRACTION97
4.1271-66.61620.26961570.18795073X-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)
13.01050.28541.59882.26570.70935.42780.0119-0.4538-0.26990.05840.09510.05850.2248-0.1357-0.10940.2874-0.1020.04290.67070.03990.21935.7699-2.0767-5.0771
21.97840.29670.08782.1041-0.3361.704-0.03710.19760.0285-0.0386-0.1189-0.434-0.06990.21580.140.3059-0.09140.01760.64340.03070.2573-5.7954-2.89730.9295
32.6122-0.3355-1.68922.1714-0.71553.9182-0.0232-0.02680.11420.15540.05780.29560.1774-0.2016-0.05880.2573-0.03620.00310.52640.06060.2348-23.30298.277919.9559
40.5567-0.1709-0.3020.9028-0.58754.6-0.0085-0.2204-0.07350.1837-0.0814-0.1031-0.05020.30560.06990.3225-0.062-0.03380.6654-0.05310.24422.86417.65726.2113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 16 through 203)
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 203)
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 203)
4X-RAY DIFFRACTION4(chain 'D' and resid 8 through 203)

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