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- PDB-1v1g: Structure of the Arabidopsis thaliana SOS3 complexed with Calcium... -

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Basic information

Entry
Database: PDB / ID: 1v1g
TitleStructure of the Arabidopsis thaliana SOS3 complexed with Calcium(II) ion
ComponentsCALCINEURIN B-LIKE PROTEIN 4
KeywordsSIGNALLING PROTEIN / SALT STRESS RESPONSE IN PLANTS / CALCINEURIN B-LIKE PROTEIN / PROTEIN CRYSTALLOGRAPHY / CALCIUM SENSOR / EF-HAND
Function / homology
Function and homology information


hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / calcineurin complex / intracellular potassium ion homeostasis / detection of calcium ion / calcium-mediated signaling / kinase binding / calcium ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Calcineurin B-like / EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Calcineurin B-like protein 4
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSanchez-Barrena, M.J. / Martinez-Ripoll, M. / Zhu, J.K. / Albert, A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Structure of the Arabidopsis Thaliana SOS3: Molecular Mechanism of Sensing Calcium for Salt Stress Response
Authors: Sanchez-Barrena, M.J. / Martinez-Ripoll, M. / Zhu, J.K. / Albert, A.
History
DepositionApr 15, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALCINEURIN B-LIKE PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,01314
Polymers25,7281
Non-polymers1,28513
Water72140
1
A: CALCINEURIN B-LIKE PROTEIN 4
hetero molecules

A: CALCINEURIN B-LIKE PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,02728
Polymers51,4572
Non-polymers2,57026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.600, 91.600, 85.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsTHE QUATERNARY STRUCTURE DESCRIPTION FOR THIS ENTRYWAS PROVIDED BY THE DEPOSITORS

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Components

#1: Protein CALCINEURIN B-LIKE PROTEIN 4 / SALT OVERLY SENSITIVE 3 (SOS3)


Mass: 25728.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O81223
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growMethod: vapor diffusion / pH: 4.8
Details: PRIOR TO CRYSTALLIZATION THE PROTEIN WAS PREINCUBATED WITH 3.8 MM CACL2 TO REACH A FINAL PROTEIN CONCENTRATION OF 10 MG/ML AND A PRTEIN:METAL ION RATIO 1:10. CRYSTALLIZATION EXPERIMENTS WERE ...Details: PRIOR TO CRYSTALLIZATION THE PROTEIN WAS PREINCUBATED WITH 3.8 MM CACL2 TO REACH A FINAL PROTEIN CONCENTRATION OF 10 MG/ML AND A PRTEIN:METAL ION RATIO 1:10. CRYSTALLIZATION EXPERIMENTS WERE CARRIED OUT AT ROOM TEMPERATURE. CRYSTALS WERE GROWN USING VAPOUR DIFFUSION TECHNIQUES FROM DROPS CONTAINING SOS3-CA, RESERVOIR SOLUTIONS (24%(W/V) METHYL-PENTANEDIOL, 18%(W/V) POLYETHYLENE GLYCOL 4000 AND 0.1 NA-CITRATE PH 4.8) AND NAI 1M IN A RATIO 2:1:0.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.92
DetectorDate: Oct 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→62 Å / Num. obs: 9757 / % possible obs: 100 % / Observed criterion σ(I): 1.4 / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 4.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.759 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.495 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM A1 - A14 AND FROM A203 - A222 ARE NOT INCLUDED IN THE MODEL. THE LOOP FROM A67 - A75 DISPLAYS POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 507 5.2 %RANDOM
Rwork0.235 ---
obs0.237 9213 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 27 40 1614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221593
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9762149
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3535187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021195
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.2819
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8441.5940
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66421528
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2643653
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.084.5621
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 38
Rwork0.419 669

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