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- PDB-4v29: The crystal structure of Arabidopsis thaliana CAR4 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4v29
TitleThe crystal structure of Arabidopsis thaliana CAR4 in complex with two calcium ions
ComponentsAT3G17980
KeywordsCALCIUM BINDING PROTEIN / LIPID 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
Protein C2-DOMAIN ABA-RELATED 4
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.6 Å
AuthorsDiaz, M. / Albert, A.
CitationJournal: Plant Cell / Year: 2014
Title: C2-Domain Abscisic Acid-Related Proteins Mediate the Interaction of Pyr/Pyl/Rcar Abscisic Acid Receptors with the Plasma Membrane and Regulate Abscisic Acid Sensitivity in Arabidopsis.
Authors: Rodriguez, L. / Gonzalez-Guzman, M. / Diaz, M. / Rodrigues, A. / Izquierdo-Garcia, A.C. / Peirats-Llobet, M. / Fernandez, M.A. / Antoni, R. / Fernandez, D. / Marquez, J.A. / Mulet, J.M. / ...Authors: Rodriguez, L. / Gonzalez-Guzman, M. / Diaz, M. / Rodrigues, A. / Izquierdo-Garcia, A.C. / Peirats-Llobet, M. / Fernandez, M.A. / Antoni, R. / Fernandez, D. / Marquez, J.A. / Mulet, J.M. / Albert, A. / Rodriguez, P.L.
History
DepositionOct 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)40,0126
Polymers39,8522
Non-polymers1604
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-6.5 kcal/mol
Surface area20580 Å2
MethodPQS
Unit cell
Length a, b, c (Å)34.848, 88.137, 108.760
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


Mass: 19926.002 Da / Num. of mol.: 2
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE
Crystal growDetails: 20% PEG 6K, 0.1 MES PH6, 0.2 M LICL

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.6→46.28 Å / Num. obs: 84856 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 99.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 37.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.6→46.3 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 4291 5.06 %
Rwork0.1942 --
obs0.1955 84856 99.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.186 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å20 Å2
2---2.5558 Å20 Å2
3----1.3242 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 4 386 3006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062652
X-RAY DIFFRACTIONf_angle_d1.0923586
X-RAY DIFFRACTIONf_dihedral_angle_d14.4821022
X-RAY DIFFRACTIONf_chiral_restr0.074424
X-RAY DIFFRACTIONf_plane_restr0.005456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.29981260.2462518X-RAY DIFFRACTION93
1.6182-1.63720.28111480.25712540X-RAY DIFFRACTION95
1.6372-1.65720.31611240.25022710X-RAY DIFFRACTION97
1.6572-1.67820.27551360.23832622X-RAY DIFFRACTION99
1.6782-1.70030.24621610.21982702X-RAY DIFFRACTION100
1.7003-1.72360.25641290.21112696X-RAY DIFFRACTION100
1.7236-1.74820.24891430.21782742X-RAY DIFFRACTION100
1.7482-1.77430.24741540.22132650X-RAY DIFFRACTION100
1.7743-1.8020.26091600.21672664X-RAY DIFFRACTION100
1.802-1.83160.27971350.21732744X-RAY DIFFRACTION100
1.8316-1.86310.23441270.19662719X-RAY DIFFRACTION100
1.8631-1.8970.21841380.20862712X-RAY DIFFRACTION100
1.897-1.93350.26241670.20522728X-RAY DIFFRACTION100
1.9335-1.9730.24351470.20142631X-RAY DIFFRACTION100
1.973-2.01590.24261240.19562736X-RAY DIFFRACTION100
2.0159-2.06280.24481510.20512711X-RAY DIFFRACTION100
2.0628-2.11440.2171450.19682671X-RAY DIFFRACTION100
2.1144-2.17150.20681620.19022712X-RAY DIFFRACTION100
2.1715-2.23540.20491550.18992650X-RAY DIFFRACTION100
2.2354-2.30760.25141350.19262734X-RAY DIFFRACTION100
2.3076-2.390.1911490.19072695X-RAY DIFFRACTION100
2.39-2.48570.24321450.20052731X-RAY DIFFRACTION100
2.4857-2.59880.20851390.19942682X-RAY DIFFRACTION100
2.5988-2.73590.21981210.19872725X-RAY DIFFRACTION100
2.7359-2.90720.25641470.19882733X-RAY DIFFRACTION100
2.9072-3.13170.22831300.19772701X-RAY DIFFRACTION100
3.1317-3.44670.19141500.18062688X-RAY DIFFRACTION100
3.4467-3.94520.16191390.1692697X-RAY DIFFRACTION100
3.9452-4.96970.16241440.15392720X-RAY DIFFRACTION100
4.9697-46.29930.221600.20132601X-RAY DIFFRACTION98

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