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- PDB-3udb: Crystal structure of SnRK2.6 -

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Basic information

Entry
Database: PDB / ID: 3udb
TitleCrystal structure of SnRK2.6
ComponentsSerine/threonine-protein kinase SRK2E
KeywordsTRANSFERASE / SnRK2.6 / kinase / ABA signaling pathway / ABI1
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: 2.567 Å
AuthorsXie, T. / Ren, R. / Pang, Y. / Yan, C.
CitationJournal: to be published
Title: Molecular mechanism for the inhibition of a critical component in the Arabidopsis thaliana abscisic acid signal transduction pathways, SnRK2.6, by the protein phosphatase ABI1
Authors: Xie, T. / Ren, R. / Pang, Y. / Yan, C.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase SRK2E
B: Serine/threonine-protein kinase SRK2E
C: Serine/threonine-protein kinase SRK2E
D: Serine/threonine-protein kinase SRK2E
E: Serine/threonine-protein kinase SRK2E
F: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,09412
Polymers215,8816
Non-polymers2136
Water2,324129
1
A: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0162
Polymers35,9801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0162
Polymers35,9801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0162
Polymers35,9801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0162
Polymers35,9801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0162
Polymers35,9801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0162
Polymers35,9801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Serine/threonine-protein kinase SRK2E
C: Serine/threonine-protein kinase SRK2E
D: Serine/threonine-protein kinase SRK2E
F: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0628
Polymers143,9214
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-59 kcal/mol
Surface area49540 Å2
MethodPISA
8
B: Serine/threonine-protein kinase SRK2E
E: Serine/threonine-protein kinase SRK2E
hetero molecules

B: Serine/threonine-protein kinase SRK2E
E: Serine/threonine-protein kinase SRK2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0628
Polymers143,9214
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7090 Å2
ΔGint-71 kcal/mol
Surface area49820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.094, 98.793, 113.103
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number5
Space group name H-MC121

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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: 35980.152 Da / Num. of mol.: 6 / Fragment: residues 1-317 / Mutation: S7A/S29A/S43A/C131A/C137A/C159A/S166A/T176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SNRK2.6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q940H6, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 19% PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03887 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03887 Å / Relative weight: 1
ReflectionResolution: 2.567→40 Å / Num. all: 78743 / Num. obs: 78271 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 49.75 Å2
Reflection shellResolution: 2.58→2.67 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FH9

2fh9


Resolution: 2.567→37.076 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.7649 / SU ML: 0.82 / σ(F): 1.34 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 3929 5.02 %RANDOM
Rwork0.2364 ---
all0.2378 78743 --
obs0.2376 78250 98.36 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.958 Å2 / ksol: 0.291 e/Å3
Displacement parametersBiso max: 200.75 Å2 / Biso mean: 61.3777 Å2 / Biso min: 16.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.2037 Å20 Å2-4.9171 Å2
2---9.396 Å2-0 Å2
3---6.7274 Å2
Refinement stepCycle: LAST / Resolution: 2.567→37.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13030 0 6 129 13165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113338
X-RAY DIFFRACTIONf_angle_d1.59618033
X-RAY DIFFRACTIONf_chiral_restr0.1041992
X-RAY DIFFRACTIONf_plane_restr0.0142334
X-RAY DIFFRACTIONf_dihedral_angle_d20.4915035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5667-2.5980.4232880.33171934202271
2.598-2.63090.39851290.350526642793100
2.6309-2.66550.38771430.350526872830100
2.6655-2.7020.39751310.33526692800100
2.702-2.74060.36891380.307326842822100
2.7406-2.78150.32761590.292726712830100
2.7815-2.82490.33821560.282726932849100
2.8249-2.87120.30151240.27726602784100
2.8712-2.92070.31081360.276626822818100
2.9207-2.97380.34861440.275726772821100
2.9738-3.03090.31071360.285926972833100
3.0309-3.09280.30371080.271726932801100
3.0928-3.160.31671350.27826892824100
3.16-3.23350.29761510.276126822833100
3.2335-3.31430.27741280.283526952823100
3.3143-3.40380.3181360.272527072843100
3.4038-3.50390.30441550.268626572812100
3.5039-3.61690.28821400.257426672807100
3.6169-3.74610.25991330.23252707284099
3.7461-3.89590.24241320.21542694282699
3.8959-4.0730.23781490.20392657280699
4.073-4.28750.20061390.18762692283199
4.2875-4.55560.21681520.17652683283599
4.5556-4.90660.1891670.17132624279199
4.9066-5.39910.25191600.21312702286299
5.3991-6.17720.25091470.24722684283199
6.1772-7.77080.20971580.20932680283899
7.7708-37.07940.21061550.21222690284597
Refinement TLS params.Method: refined / Origin x: -40.569 Å / Origin y: -8.5337 Å / Origin z: 32.6509 Å
111213212223313233
T0.221 Å20.0109 Å2-0.0185 Å2-0.1687 Å20.0063 Å2--0.2122 Å2
L0.1472 °20.0136 °20.0533 °2-0.1675 °20.067 °2--0.159 °2
S0.0118 Å °0.0171 Å °0.0303 Å °-0.0629 Å °0.0199 Å °-0.0351 Å °0.0268 Å °0.0019 Å °-0.0285 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 317
2X-RAY DIFFRACTION1allB12 - 317
3X-RAY DIFFRACTION1allC12 - 317
4X-RAY DIFFRACTION1allD12 - 317
5X-RAY DIFFRACTION1allE13 - 316
6X-RAY DIFFRACTION1allF12 - 317
7X-RAY DIFFRACTION1allD - B1 - 350
8X-RAY DIFFRACTION1allC - E1 - 318

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