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- PDB-5a50: The crystal structure of Arabidopsis thaliana CAR4 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5a50
TitleThe crystal structure of Arabidopsis thaliana CAR4 in complex with two calcium ions, Zn and Phopho Choline
Components(AT3G17980) x 2
KeywordsLIPID BINDING PROTEIN / CALCIUM BINDING PROTEIN / C2 DOMAIN
Function / homology
Function and homology information


positive regulation of response to salt stress / positive regulation of abscisic acid-activated signaling pathway / positive regulation of defense response to bacterium / abscisic acid-activated signaling pathway / response to salt stress / GTPase activator activity / positive regulation of GTPase activity / phospholipid binding / defense response / : ...positive regulation of response to salt stress / positive regulation of abscisic acid-activated signaling pathway / positive regulation of defense response to bacterium / abscisic acid-activated signaling pathway / response to salt stress / GTPase activator activity / positive regulation of GTPase activity / phospholipid binding / defense response / : / lipid binding / calcium ion binding / protein homodimerization activity / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein C2-DOMAIN ABA-RELATED / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
PHOSPHOCHOLINE / Protein C2-DOMAIN ABA-RELATED 4
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDiaz, M. / Albert, 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 2.0Jun 14, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.type_symbol / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.symmetry
Revision 2.1Jan 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
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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AT3G17980
B: AT3G17980
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3209
Polymers39,7262
Non-polymers5947
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-84.2 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.737, 89.150, 112.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9992, 0.03148, -0.02437), (0.03314, -0.9969, 0.07112), (-0.02206, -0.07187, -0.9972)
Vector: 1.244, 3.077, -44.2)

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein AT3G17980 / CAR4


Mass: 19883.898 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: Q9LVH4
#2: Protein AT3G17980 / CAR4


Mass: 19841.799 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: Q9LVH4

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Non-polymers , 4 types, 148 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H15NO4P
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.26 Å3/Da / Density % sol: 45.46 % / Description: NONE
Crystal growDetails: 20 TO 25 % OF POLYETHYLENE GLYCOL 6K, 0.1M MES PH 6.0 TO 6.5 ZNCL2 5MM POC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.4→47.5 Å / Num. obs: 27044 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.3 / % possible all: 99

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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: 2.4→47.564 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 1339 4.9 %
Rwork0.1946 --
obs0.1971 27044 99.75 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 27 141 2775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082663
X-RAY DIFFRACTIONf_angle_d1.2273607
X-RAY DIFFRACTIONf_dihedral_angle_d18.4341029
X-RAY DIFFRACTIONf_chiral_restr0.044424
X-RAY DIFFRACTIONf_plane_restr0.004456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.29191360.26792526X-RAY DIFFRACTION100
2.4858-2.58530.31861270.25882598X-RAY DIFFRACTION100
2.5853-2.7030.32371230.25632566X-RAY DIFFRACTION100
2.703-2.84550.31351400.242580X-RAY DIFFRACTION100
2.8455-3.02370.23881210.22912618X-RAY DIFFRACTION100
3.0237-3.25710.34751240.21452584X-RAY DIFFRACTION100
3.2571-3.58480.21771300.19212587X-RAY DIFFRACTION100
3.5848-4.10330.22671410.17292535X-RAY DIFFRACTION100
4.1033-5.16870.20841320.14342586X-RAY DIFFRACTION100
5.1687-47.57380.18541650.15982525X-RAY DIFFRACTION99

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