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- PDB-2zfd: The crystal structure of plant specific calcium binding protein A... -

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Basic information

Entry
Database: PDB / ID: 2zfd
TitleThe crystal structure of plant specific calcium binding protein AtCBL2 in complex with the regulatory domain of AtCIPK14
Components
  • Calcineurin B-like protein 2
  • Putative uncharacterized protein T20L15_90
KeywordsSIGNALING PROTEIN/TRANSFERASE / calcium binding protein / protein-protein complex / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Transferase / SIGNALING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


plant-type vacuole membrane / response to water deprivation / plasmodesma / response to abscisic acid / plant-type vacuole / potassium ion homeostasis / vacuole / plastid / response to glucose / cytosolic ribosome ...plant-type vacuole membrane / response to water deprivation / plasmodesma / response to abscisic acid / plant-type vacuole / potassium ion homeostasis / vacuole / plastid / response to glucose / cytosolic ribosome / response to salt stress / response to cold / calcium-mediated signaling / kinase binding / response to heat / response to oxidative stress / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / calcium ion binding / signal transduction / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
NAF domain / NAF/FISL domain / NAF domain / NAF domain profile. / Calcineurin B-like / Kinase associated domain 1, KA1 / EF hand / TATA-Binding Protein / EF-hand domain pair / EF-hand ...NAF domain / NAF/FISL domain / NAF domain / NAF domain profile. / Calcineurin B-like / Kinase associated domain 1, KA1 / EF hand / TATA-Binding Protein / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Calcineurin B-like protein 2 / CBL-interacting serine/threonine-protein kinase 14
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsAkaboshi, M. / Hashimoto, H. / Ishida, H. / Koizumi, N. / Sato, M. / Shimizu, T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The crystal structure of plant-specific calcium-binding protein AtCBL2 in complex with the regulatory domain of AtCIPK14
Authors: Akaboshi, M. / Hashimoto, H. / Ishida, H. / Saijo, S. / Koizumi, N. / Sato, M. / Shimizu, T.
History
DepositionDec 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: Calcineurin B-like protein 2
B: Putative uncharacterized protein T20L15_90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,25710
Polymers39,8962
Non-polymers3618
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-85.5 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.092, 45.481, 92.390
Angle α, β, γ (deg.)90.00, 92.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calcineurin B-like protein 2 / SOS3-like calcium-binding protein 1


Mass: 25841.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CBL2 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LAS7
#2: Protein Putative uncharacterized protein T20L15_90 / Putative uncharacterized protein At5g01820 / CBL-interacting protein kinase 14 / Serine/threonine ...Putative uncharacterized protein At5g01820 / CBL-interacting protein kinase 14 / Serine/threonine protein kinase


Mass: 14055.048 Da / Num. of mol.: 1 / Fragment: UNP residues 305-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CIPK14 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LZW4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 31.86 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9796, 0.9798, 0.9645
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 11, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97981
30.96451
ReflectionResolution: 1.2→50 Å / Num. obs: 85565 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.431 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.128 / SU ML: 0.024 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19162 4271 5 %RANDOM
Rwork0.17971 ---
obs0.18032 80720 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.18 Å2
2--0.03 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 14 236 2637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222452
X-RAY DIFFRACTIONr_bond_other_d0.0010.021666
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9553307
X-RAY DIFFRACTIONr_angle_other_deg0.85634063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31624.622119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.73615448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1331515
X-RAY DIFFRACTIONr_chiral_restr0.0710.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
X-RAY DIFFRACTIONr_nbd_refined0.2330.2529
X-RAY DIFFRACTIONr_nbd_other0.1810.21703
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21235
X-RAY DIFFRACTIONr_nbtor_other0.0830.21203
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2159
X-RAY DIFFRACTIONr_metal_ion_refined0.090.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0790.23
X-RAY DIFFRACTIONr_mcbond_it0.81.51557
X-RAY DIFFRACTIONr_mcbond_other0.1741.5606
X-RAY DIFFRACTIONr_mcangle_it1.1822410
X-RAY DIFFRACTIONr_scbond_it1.88731021
X-RAY DIFFRACTIONr_scangle_it2.7954.5896
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 294 -
Rwork0.201 5593 -
obs--90.78 %
Refinement TLS params.Method: refined / Origin x: 31.1778 Å / Origin y: 8.5398 Å / Origin z: 21.8775 Å
111213212223313233
T-0.0122 Å2-0.0071 Å2-0.0015 Å2--0.0107 Å2-0.0016 Å2---0.0114 Å2
L0.2273 °2-0.004 °2-0.0399 °2-0.1506 °20.0402 °2--0.1646 °2
S0.0146 Å °-0.0314 Å °0.0158 Å °0.0317 Å °0.0006 Å °-0.0159 Å °-0.0151 Å °0.0219 Å °-0.0152 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 221
2X-RAY DIFFRACTION1A234 - 385
3X-RAY DIFFRACTION1B2
4X-RAY DIFFRACTION1A227 - 233
5X-RAY DIFFRACTION1B308 - 426
6X-RAY DIFFRACTION1A32 - 214

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