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- PDB-3zut: The structure of OST1 (D160A) kinase -

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Basic information

Entry
Database: PDB / ID: 3zut
TitleThe structure of OST1 (D160A) kinase
ComponentsSerine/threonine-protein kinase SRK2E
KeywordsTRANSFERASE / KINASE REGULATION / PLANT ABIOTIC STRESS / SIGNALING
Function / homology
Function and homology information


cellular response to absence of light / regulation of anion channel activity / regulation of stomatal opening / triglyceride biosynthetic process / cellular response to carbon dioxide / unsaturated fatty acid biosynthetic process / positive regulation of abscisic acid-activated signaling pathway / sucrose metabolic process / regulation of stomatal closure / stomatal movement ...cellular response to absence of light / regulation of anion channel activity / regulation of stomatal opening / triglyceride biosynthetic process / cellular response to carbon dioxide / unsaturated fatty acid biosynthetic process / positive regulation of abscisic acid-activated signaling pathway / sucrose metabolic process / regulation of stomatal closure / stomatal movement / leaf development / regulation of stomatal movement / calcium-dependent protein serine/threonine kinase activity / response to abscisic acid / response to water deprivation / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / entity_src_nat / refine / struct_ref
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.pdbx_mutation / _entity.src_method / _entity_name_com.name / _refine.pdbx_starting_model / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)82,1052
Polymers82,1052
Non-polymers00
Water1,06359
1
A: Serine/threonine-protein kinase SRK2E


Theoretical massNumber of molelcules
Total (without water)41,0521
Polymers41,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase SRK2E


Theoretical massNumber of molelcules
Total (without water)41,0521
Polymers41,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.273, 99.195, 107.832
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: (0.6152, 0.3246, 0.7184), (0.3222, -0.9353, 0.1466), (0.7195, 0.1412, -0.68)
Vector: -14.17, 31.3, 17.37)

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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: 41052.492 Da / Num. of mol.: 2 / Mutation: D160A
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
References: UniProt: Q940H6, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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

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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: 2.54 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH 6.5, 12% PEG10000 AND 12% ETHYLENE GLYCOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→41.74 Å / Num. obs: 29227 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HYH

3hyh


Resolution: 2.5→41.74 Å / SU ML: 0.8 / σ(F): 0 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1470 5 %
Rwork0.1975 --
obs0.2002 29227 99.55 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.43 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3054 Å20 Å20 Å2
2---2.8487 Å20 Å2
3---4.1541 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 0 59 4582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014627
X-RAY DIFFRACTIONf_angle_d1.0786260
X-RAY DIFFRACTIONf_dihedral_angle_d15.9751754
X-RAY DIFFRACTIONf_chiral_restr0.067687
X-RAY DIFFRACTIONf_plane_restr0.006812
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1064X-RAY DIFFRACTIONPOSITIONAL
12B1064X-RAY DIFFRACTIONPOSITIONAL0.065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58940.40031250.32592757X-RAY DIFFRACTION100
2.5894-2.69310.34881230.28012760X-RAY DIFFRACTION100
2.6931-2.81560.30841530.24522715X-RAY DIFFRACTION100
2.8156-2.9640.28691490.23632758X-RAY DIFFRACTION100
2.964-3.14970.28021310.22022767X-RAY DIFFRACTION100
3.1497-3.39280.29031440.222766X-RAY DIFFRACTION100
3.3928-3.7340.25341510.20172757X-RAY DIFFRACTION100
3.734-4.27390.23181650.17192788X-RAY DIFFRACTION100
4.2739-5.38280.20171770.15172771X-RAY DIFFRACTION99
5.3828-41.74530.24321520.19092918X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.08381.36271.13234.51780.80115.27870.28390.4015-0.42131.1963-0.0471-0.1295-0.54490.3457-0.17360.92550.16580.15530.46120.08570.516418.578242.539423.8259
20.4818-0.3855-0.26974.0129-0.81561.24570.09810.013-0.02440.389-0.04940.3359-0.3291-0.0807-0.04180.36260.04670.02930.39050.0570.383720.850335.523110.8686
33.2936-0.7319-0.02441.2614-0.10022.130.16870.19810.3649-0.0923-0.11690.1212-0.26970.1177-0.09630.388-0.00060.01490.26020.02910.321430.771527.34744.2735
42.96451.4671-0.71093.2604-0.47362.9230.18030.1743-0.4715-0.378-0.18480.01120.40750.2798-0.01840.3370.0734-0.00180.1861-0.04610.291533.154915.13481.1031
55.49110.48720.7522.96941.05435.55370.433-1.085-0.22480.0111-0.51010.32531.095-1.2459-0.03180.6212-0.0435-0.07580.52550.12410.719127.46011.022120.3061
62.0085-0.564-1.12382.54531.80782.7255-0.0074-0.1567-0.41870.2084-0.1193-0.12990.5042-0.17350.08850.4168-0.0623-0.00110.43290.11720.430518.03916.281730.0311
73.09410.86520.86633.20252.70093.47360.0952-0.1763-0.41460.31660.0444-0.24010.4258-0.3748-0.2210.30680.00840.08180.44820.15020.386817.345316.546940.1348
82.4515-0.13890.63751.42970.46142.72390.1888-0.20180.40950.0834-0.09510.3316-0.5533-0.7483-0.07680.46660.12860.14490.58560.07510.402511.770328.123442.6538
95.11210.05561.28424.57790.67757.4030.19640.26640.9681-0.1842-0.1963-0.1554-1.80290.44340.25940.96640.16220.10570.40070.18850.520819.805854.95019.1491
105.9088-1.22180.50976.76360.85432.8671-0.2295-0.357-0.75860.3887-0.75970.12970.5010.0910.26371.0935-0.08460.09290.56430.47251.456522.2279-13.058432.994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 10:34)
2X-RAY DIFFRACTION2CHAIN A'AND (RESSEQ 35:133)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 134:212)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 213:285)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 12:34)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 35:133)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 134:212)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 213:285)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 301:319)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 301:319)

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