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- PDB-3zuu: The structure of OST1 (D160A, S175D) kinase in complex with gold -

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Basic information

Entry
Database: PDB / ID: 3zuu
TitleThe structure of OST1 (D160A, S175D) kinase in complex with gold
ComponentsSerine/threonine-protein kinase SRK2E
KeywordsTRANSFERASE / KINASE REGULATION / SIGNALING
Function / homology
Function and homology information


cellular response to absence of light / regulation of anion channel activity / regulation of stomatal opening / unsaturated fatty acid biosynthetic process / triglyceride biosynthetic process / positive regulation of abscisic acid-activated signaling pathway / sucrose metabolic process / regulation of stomatal closure / cellular response to carbon dioxide / stomatal movement ...cellular response to absence of light / regulation of anion channel activity / regulation of stomatal opening / unsaturated fatty acid biosynthetic process / triglyceride biosynthetic process / positive regulation of abscisic acid-activated signaling pathway / sucrose metabolic process / regulation of stomatal closure / cellular response to carbon dioxide / stomatal movement / leaf development / regulation of stomatal movement / calcium-dependent protein serine/threonine kinase activity / response to water deprivation / response to abscisic acid / abscisic acid-activated signaling pathway / regulation of reactive oxygen species metabolic process / response to osmotic stress / response to salt stress / kinase activity / protein phosphatase binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / defense response to bacterium / protein serine kinase activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
: / Serine/threonine-protein kinase SRK2E
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsYunta, C. / Martinez-Ripoll, M. / Albert, A.
CitationJournal: J. Mol. Biol. / Year: 2011
Title: The structure of Arabidopsis thaliana OST1 provides insights into the kinase regulation mechanism in response to osmotic stress.
Authors: Yunta, C. / Martinez-Ripoll, M. / Zhu, J.K. / Albert, A.
History
DepositionJul 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Oct 24, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.3May 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 / 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 / _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: Serine/threonine-protein kinase SRK2E
B: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4825
Polymers82,1612
Non-polymers3213
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-10.5 kcal/mol
Surface area32010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.570, 99.017, 108.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 90:132 OR RESSEQ 156:159 OR RESSEQ 194:220 OR RESSEQ 228:286)
211CHAIN B AND (RESSEQ 90:132 OR RESSEQ 156:159 OR RESSEQ 194:220 OR RESSEQ 228:286)

NCS oper: (Code: given
Matrix: (0.6154, 0.3304, 0.7156), (0.3294, -0.9326, 0.1473), (0.7161, 0.145, -0.6828)
Vector: -14.28, 30.77, 17.56)

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Components

#1: Protein Serine/threonine-protein kinase SRK2E / Protein OPEN STOMATA 1 / SNF1-related kinase 2.6 / SnRK2.6 / Serine/threonine-protein kinase OST1


Mass: 41080.504 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SRK2E, OST1, SNRK2.6, At4g33950, F17I5.140 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS
References: UniProt: Q940H6, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 160 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 160 TO ALA
Sequence detailsMUTATIONS D160A S175D ENGINEERED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 0.1M HEPES PH 7.0, 14% PEG 10000, AND 12% ETHYLENE GLYCOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.04
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.7→77.57 Å / Num. obs: 23628 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 63.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→54.225 Å / SU ML: 0.72 / σ(F): 1.34 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 902 3.8 %
Rwork0.2383 --
obs0.2399 23608 99.94 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.61 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0899 Å20 Å20 Å2
2---6.6089 Å20 Å2
3---6.5189 Å2
Refinement stepCycle: LAST / Resolution: 2.7→54.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 9 48 4579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014633
X-RAY DIFFRACTIONf_angle_d1.1536264
X-RAY DIFFRACTIONf_dihedral_angle_d17.5931756
X-RAY DIFFRACTIONf_chiral_restr0.077687
X-RAY DIFFRACTIONf_plane_restr0.005812
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1064X-RAY DIFFRACTIONPOSITIONAL
12B1064X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.86920.33381490.32163731X-RAY DIFFRACTION100
2.8692-3.09070.33311520.28723730X-RAY DIFFRACTION100
3.0907-3.40170.32281600.27723718X-RAY DIFFRACTION100
3.4017-3.89390.28361460.24593753X-RAY DIFFRACTION100
3.8939-4.90530.25011600.19983798X-RAY DIFFRACTION100
4.9053-54.23640.26411350.2263976X-RAY DIFFRACTION100

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