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- PDB-5a51: The crystal structure of Arabidopsis thaliana CAR4 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5a51
TitleThe crystal structure of Arabidopsis thaliana CAR4 in complex with two calcium ions and phophatidyl serine
ComponentsAT3G17980
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
PHOSPHOSERINE / Protein C2-DOMAIN ABA-RELATED 4
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 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 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)40,1977
Polymers39,8522
Non-polymers3455
Water9,566531
1
A: AT3G17980
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0063
Polymers19,9261
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AT3G17980
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1914
Polymers19,9261
Non-polymers2653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.583, 89.769, 109.642
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: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.2 Å3/Da / Density % sol: 44.01 % / Description: NONE
Crystal growDetails: FROM 20 TO 25 % OF POLYETHYLENE GLYCOL 6K, 0.1M MES PH 6.0 TO 6.5 AND 0.1M LICL 5MM PSF

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Data collection

DiffractionMean temperature: 100 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→46.7 Å / Num. obs: 88958 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.72 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.7 / % 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: 1.602→46.787 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 4526 5.1 %
Rwork0.1923 --
obs0.1939 88958 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.278 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1154 Å20 Å20 Å2
2---2.1693 Å20 Å2
3----2.9461 Å2
Refinement stepCycle: LAST / Resolution: 1.602→46.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 15 531 3162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062662
X-RAY DIFFRACTIONf_angle_d1.0773600
X-RAY DIFFRACTIONf_dihedral_angle_d15.3041026
X-RAY DIFFRACTIONf_chiral_restr0.071425
X-RAY DIFFRACTIONf_plane_restr0.004457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6023-1.62050.26551170.24162748X-RAY DIFFRACTION96
1.6205-1.63960.27441880.23352727X-RAY DIFFRACTION100
1.6396-1.65960.23751310.22992859X-RAY DIFFRACTION100
1.6596-1.68060.25631650.21952806X-RAY DIFFRACTION100
1.6806-1.70270.20881500.20022845X-RAY DIFFRACTION100
1.7027-1.7260.2591500.20982770X-RAY DIFFRACTION100
1.726-1.75070.23061820.20752799X-RAY DIFFRACTION100
1.7507-1.77680.30191320.19432878X-RAY DIFFRACTION100
1.7768-1.80460.21681150.19412829X-RAY DIFFRACTION100
1.8046-1.83420.22151800.19722757X-RAY DIFFRACTION100
1.8342-1.86580.25821730.18742874X-RAY DIFFRACTION100
1.8658-1.89970.27981470.19332761X-RAY DIFFRACTION100
1.8997-1.93630.21471360.20362840X-RAY DIFFRACTION100
1.9363-1.97580.25661430.1882875X-RAY DIFFRACTION100
1.9758-2.01880.26581520.20032775X-RAY DIFFRACTION100
2.0188-2.06570.26321500.19642831X-RAY DIFFRACTION100
2.0657-2.11740.21981100.18882878X-RAY DIFFRACTION100
2.1174-2.17460.21931450.18992794X-RAY DIFFRACTION100
2.1746-2.23860.2351380.1942864X-RAY DIFFRACTION100
2.2386-2.31090.24391530.18732788X-RAY DIFFRACTION100
2.3109-2.39350.23311710.19152841X-RAY DIFFRACTION100
2.3935-2.48930.22381720.19472783X-RAY DIFFRACTION100
2.4893-2.60260.2491410.20652830X-RAY DIFFRACTION100
2.6026-2.73980.2471590.21072843X-RAY DIFFRACTION100
2.7398-2.91140.21641740.19432764X-RAY DIFFRACTION100
2.9114-3.13620.21681350.18932816X-RAY DIFFRACTION100
3.1362-3.45170.18381440.1752838X-RAY DIFFRACTION100
3.4517-3.95090.15021660.17292835X-RAY DIFFRACTION100
3.9509-4.97680.1731450.16222815X-RAY DIFFRACTION100
4.9768-46.80650.24891620.21562769X-RAY DIFFRACTION99

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