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- PDB-5a52: The crystal structure of Arabidopsis thaliana CAR1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5a52
TitleThe crystal structure of Arabidopsis thaliana CAR1 in complex with one calcium ion
ComponentsCALCIUM-DEPENDENT LIPID-BINDING DOMAIN-CONTAINING PROTEIN
KeywordsLIPID BINDING PROTEIN / CALCIUM BINDING PROTEIN / C2 DOMAIN
Function / homology
Function and homology information


positive regulation of abscisic acid-activated signaling pathway / abscisic acid-activated signaling pathway / GTPase activator activity / phospholipid binding / calcium ion binding / lipid binding / protein homodimerization activity / nucleus / plasma membrane
Similarity search - Function
Protein C2-DOMAIN ABA-RELATED / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Protein C2-DOMAIN ABA-RELATED 1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFernandez, D. / Marquez, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Calcium-Dependent Oligomerization of Car Proteins at Cell Membrane Modulates Aba Signaling.
Authors: Diaz, M. / Sanchez-Barrena, M.J. / Gonzalez-Rubio, J.M. / Rodriguez, L. / Fernandez, D. / Antoni, R. / Yunta, C. / Belda-Palazon, B. / Gonzalez-Guzman, M. / Peirats-Llobet, M. / Menendez, M. ...Authors: Diaz, M. / Sanchez-Barrena, M.J. / Gonzalez-Rubio, J.M. / Rodriguez, L. / Fernandez, D. / Antoni, R. / Yunta, C. / Belda-Palazon, B. / Gonzalez-Guzman, M. / Peirats-Llobet, M. / Menendez, M. / Boskovic, J. / Marquez, J.A. / Rodriguez, P.L. / Albert, A.
History
DepositionJun 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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.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: CALCIUM-DEPENDENT LIPID-BINDING DOMAIN-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1925
Polymers18,8681
Non-polymers3244
Water1,72996
1
A: CALCIUM-DEPENDENT LIPID-BINDING DOMAIN-CONTAINING PROTEIN
hetero molecules

A: CALCIUM-DEPENDENT LIPID-BINDING DOMAIN-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,38410
Polymers37,7362
Non-polymers6498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area2460 Å2
ΔGint-70 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.600, 170.300, 53.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CALCIUM-DEPENDENT LIPID-BINDING DOMAIN-CONTAINING PROTEIN / CAR1


Mass: 18867.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9FHP6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.38 Å3/Da / Density % sol: 48.26 % / Description: NONE
Crystal growDetails: 0.5 M MGSO4, 0.5 M HEPES PH 7.0 AND 1.6 M LITHIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→23.23 Å / Num. obs: 22034 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 21.35 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.79
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V29

4v29


Resolution: 1.65→23.231 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1102 5 %
Rwork0.2131 --
obs0.2146 22034 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→23.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 17 96 1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081253
X-RAY DIFFRACTIONf_angle_d1.2471698
X-RAY DIFFRACTIONf_dihedral_angle_d16.184467
X-RAY DIFFRACTIONf_chiral_restr0.053194
X-RAY DIFFRACTIONf_plane_restr0.005215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6503-1.72540.26011330.2552526X-RAY DIFFRACTION99
1.7254-1.81630.30591360.24142586X-RAY DIFFRACTION100
1.8163-1.930.28581360.22982594X-RAY DIFFRACTION100
1.93-2.0790.23451390.21422626X-RAY DIFFRACTION100
2.079-2.2880.21941370.20932615X-RAY DIFFRACTION100
2.288-2.61870.24531380.22172622X-RAY DIFFRACTION100
2.6187-3.29780.2611410.2232671X-RAY DIFFRACTION100
3.2978-23.23370.22691420.19562692X-RAY DIFFRACTION97

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