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- PDB-5aar: Structure of the ankyrin domain of an Arabidopsis Thaliana potass... -

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Basic information

Entry
Database: PDB / ID: 5aar
TitleStructure of the ankyrin domain of an Arabidopsis Thaliana potassium channel
ComponentsPOTASSIUM CHANNEL AKT1
KeywordsTRANSPORT PROTEIN / ANKYRIN / ABIOTIC STRESS / ION HOMEOSTASIS
Function / homology
Function and homology information


root hair elongation / regulation of stomatal closure / response to water deprivation / inward rectifier potassium channel activity / monoatomic ion channel complex / potassium ion import across plasma membrane / response to salt stress / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Ankyrin repeat-containing domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Ankyrin repeat-containing domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Ankyrin repeat / RmlC-like jelly roll fold / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ion transport domain / Ion transport protein / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Potassium channel AKT1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsChaves-Sanjuan, A. / Sanchez-Barrena, M.J. / Albert, A.
CitationJournal: Plant Physiol. / Year: 2020
Title: Recognition and activation of the plant AKT1 potassium channel by the kinase CIPK23.
Authors: Sanchez-Barrena, M.J. / Chaves-Sanjuan, A. / Raddatz, N. / Mendoza, I. / Cortes, A. / Gago, F. / Gonzalez-Rubio, J.M. / Benavente, J.L. / Quintero, F.J. / Pardo, J.M. / Albert, A.
History
DepositionJul 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.status_code_sf
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: POTASSIUM CHANNEL AKT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4183
Polymers20,3691
Non-polymers492
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.921, 85.570, 65.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein POTASSIUM CHANNEL AKT1 / ARABIDOPSIS POTASSIUM TRANSPORTER 1


Mass: 20369.035 Da / Num. of mol.: 1 / Fragment: ANKYRIN REPEAT DOMAIN, RESIDUES 518-702
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 PLYSS / References: UniProt: Q38998
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.38 Å3/Da / Density % sol: 48.38 % / Description: NONE
Crystal growDetails: 0.1 M TRIS PH 8.5, 25% PEG 4000, 0.3 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.87→42.79 Å / Num. obs: 16865 / % possible obs: 99.1 % / Observed criterion σ(I): 1.1 / Redundancy: 4.5 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.8
Reflection shellResolution: 1.87→1.89 Å / Redundancy: 3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.1 / % possible all: 99.1

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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 2XEH

2xeh


Resolution: 1.87→42.785 Å / SU ML: 0.28 / σ(F): 0.16 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1563 5 %
Rwork0.1969 --
obs0.1995 16833 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→42.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 2 178 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091467
X-RAY DIFFRACTIONf_angle_d0.9731974
X-RAY DIFFRACTIONf_dihedral_angle_d13.803539
X-RAY DIFFRACTIONf_chiral_restr0.038225
X-RAY DIFFRACTIONf_plane_restr0.005262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.93040.3871260.34672560X-RAY DIFFRACTION93
1.9304-1.99940.33881600.30512649X-RAY DIFFRACTION99
1.9994-2.07940.35121240.26062760X-RAY DIFFRACTION100
2.0794-2.17410.31131670.2452693X-RAY DIFFRACTION100
2.1741-2.28870.26941640.22722700X-RAY DIFFRACTION100
2.2887-2.43210.28231800.21922689X-RAY DIFFRACTION100
2.4321-2.61980.25541610.19792702X-RAY DIFFRACTION100
2.6198-2.88340.23411090.19172786X-RAY DIFFRACTION100
2.8834-3.30050.27261340.18492726X-RAY DIFFRACTION100
3.3005-4.15780.20791300.15572732X-RAY DIFFRACTION100
4.1578-42.79620.20011080.1722758X-RAY DIFFRACTION100

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