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- PDB-5a4x: The crystal structure of Arabidopsis thaliana CAR4 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5a4x
TitleThe crystal structure of Arabidopsis thaliana CAR4 in complex with two calcium ions and Zn
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 / phospholipid binding / defense response / positive regulation of GTPase activity / : ...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 / phospholipid binding / defense response / positive regulation of GTPase activity / : / 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
Protein C2-DOMAIN ABA-RELATED 4
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 15, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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: AT3G17980
B: AT3G17980
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8937
Polymers39,6682
Non-polymers2265
Water2,162120
1
A: AT3G17980
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9643
Polymers19,8841
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AT3G17980
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9294
Polymers19,7841
Non-polymers1463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.121, 88.645, 110.090
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

#1: Protein AT3G17980 / CAR4 / C2 DOMAIN-CONTAINING PROTEIN


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 / C2 DOMAIN-CONTAINING PROTEIN


Mass: 19783.764 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
#3: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.16 Å3/Da / Density % sol: 43.06 % / Description: NONE
Crystal growpH: 7
Details: 20 TO 25 % OF POLYETHYLENE GLYCOL 6K, 0.1M MES PH 6.0 TO 6.5 0.1 M ZNCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.71
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.71 Å / Relative weight: 1
ReflectionResolution: 2.2→46.9 Å / Num. obs: 36649 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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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: 2.2→46.763 Å / SU ML: 0.73 / σ(F): 1.43 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 1684 5 %
Rwork0.2201 --
obs0.2224 33633 99.84 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.916 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.2103 Å20 Å20 Å2
2--2.2597 Å20 Å2
3----10.47 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 5 120 2665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082576
X-RAY DIFFRACTIONf_angle_d1.1013489
X-RAY DIFFRACTIONf_dihedral_angle_d17.974985
X-RAY DIFFRACTIONf_chiral_restr0.072415
X-RAY DIFFRACTIONf_plane_restr0.005444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.26480.35361540.31852630X-RAY DIFFRACTION100
2.2648-2.33790.36011470.26972690X-RAY DIFFRACTION100
2.3379-2.42150.34141290.26482631X-RAY DIFFRACTION100
2.4215-2.51840.37161400.26252723X-RAY DIFFRACTION100
2.5184-2.6330.25961570.26032592X-RAY DIFFRACTION100
2.633-2.77180.32551060.25232700X-RAY DIFFRACTION100
2.7718-2.94550.29461320.23632684X-RAY DIFFRACTION100
2.9455-3.17290.24651360.22782686X-RAY DIFFRACTION100
3.1729-3.49210.29481570.20912635X-RAY DIFFRACTION100
3.4921-3.99710.23021270.20152659X-RAY DIFFRACTION100
3.9971-5.0350.20181550.15942681X-RAY DIFFRACTION100
5.035-46.77330.24121440.21932638X-RAY DIFFRACTION100

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