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- PDB-5wax: Crystal Structure of Sugarcane SAPK10 (serine/threonine-protein k... -

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Basic information

Entry
Database: PDB / ID: 5wax
TitleCrystal Structure of Sugarcane SAPK10 (serine/threonine-protein kinase 10)
ComponentsSAPK10 (serine/threonine-protein kinase 10)
KeywordsSIGNALING PROTEIN / serine/threonine kinase / abscisic acid-related SnRK2s / PLANT PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


intracellular signal transduction / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesSaccharum officinarum complex (cultivated sugarcanes)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRighetto, G.L. / Counago, R.M. / Halabelian, L. / Santiago, A.S. / Massirer, K.B. / Arruda, P. / Gileadi, O. / Menossi, M. / Edwards, A.M. / Elkins, J.M. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of Sugarcane SAPK10 (serine/threonine-protein kinase 10)
Authors: Righetto, G.L. / Counago, R.M. / Halabelian, L. / Santiago, A.S. / Massirer, K.B. / Arruda, P. / Gileadi, O. / Menossi, M. / Edwards, A.M. / Elkins, J.M.
History
DepositionJun 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAPK10 (serine/threonine-protein kinase 10)
B: SAPK10 (serine/threonine-protein kinase 10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1716
Polymers70,8032
Non-polymers3684
Water6,972387
1
A: SAPK10 (serine/threonine-protein kinase 10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6784
Polymers35,4021
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAPK10 (serine/threonine-protein kinase 10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4942
Polymers35,4021
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.420, 214.630, 93.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 4 - 310 / Label seq-ID: 4 - 310

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsmonomer by gel filtration

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Components

#1: Protein SAPK10 (serine/threonine-protein kinase 10)


Mass: 35401.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: hybrid cultivar of Saccharum officinarum and Saccharum spontaneum
Source: (gene. exp.) Saccharum officinarum complex (cultivated sugarcanes)
Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pRARE / References: UniProt: A0A238LNS4*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5M ammonium sulfate; 0.1M bis-tris pH 6.5; 0.1M sodium chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 22, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→46.576 Å / Num. obs: 51618 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 32.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.091 / Net I/av σ(I): 15.7 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3763 / CC1/2: 0.59 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZUT

3zut


Resolution: 2→19.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.91 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23676 2567 5 %RANDOM
Rwork0.19841 ---
obs0.20038 48977 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.537 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 24 387 4771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194474
X-RAY DIFFRACTIONr_bond_other_d0.0020.024152
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9676060
X-RAY DIFFRACTIONr_angle_other_deg0.9639584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24723.285207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39415743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3941537
X-RAY DIFFRACTIONr_chiral_restr0.090.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214932
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6163.4722205
X-RAY DIFFRACTIONr_mcbond_other2.6163.4712204
X-RAY DIFFRACTIONr_mcangle_it3.9985.1792744
X-RAY DIFFRACTIONr_mcangle_other3.9985.1812745
X-RAY DIFFRACTIONr_scbond_it3.0283.7442269
X-RAY DIFFRACTIONr_scbond_other3.0273.7442269
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6865.5023317
X-RAY DIFFRACTIONr_long_range_B_refined6.76141.635148
X-RAY DIFFRACTIONr_long_range_B_other6.68941.2715063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17006 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 197 -
Rwork0.315 3525 -
obs--99.84 %

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