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- PDB-6eas: Co-crystal of pseudokinase DRIK1 (drought responsive inactive kin... -

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Basic information

Entry
Database: PDB / ID: 6eas
TitleCo-crystal of pseudokinase DRIK1 (drought responsive inactive kinase 1) bound to ENMD-2076
Componentsdrought responsive inactive kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Receptor-like kinase / pseudokinase / maize / ENMD-2076 / Structural Genomics Consortium / TRANSFERASE-TRANSFERASE INHIBITOR complex / SGC
Function / homology
Function and homology information


endomembrane system / protein kinase activity / ATP binding / membrane
Similarity search - Function
Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-J3A / Protein kinase domain-containing protein / Protein kinase superfamily protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAquino, B. / Counago, R.M. / Fala, A.M. / Massirer, K.B. / Elkins, J.M. / Arruda, P. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)13/50724-5 Brazil
CitationJournal: To be Published
Title: Co-crystal of pseudokinase DRIK1 with ENMD-2076
Authors: Aquino, B. / Counago, R.M. / Fala, A.M. / Massirer, K.B. / Elkins, J.M. / Arruda, P.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 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 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: drought responsive inactive kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2533
Polymers34,7861
Non-polymers4682
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint1 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.506, 61.790, 65.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein drought responsive inactive kinase 1 / DRIK1


Mass: 34785.602 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 183-488)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Plasmid: pNIC28a-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4F901, UniProt: C0P4K9*PLUS
#2: Chemical ChemComp-J3A / 6-(4-methylpiperazin-1-yl)-N-(5-methyl-1H-pyrazol-3-yl)-2-[(E)-2-phenylethenyl]pyrimidin-4-amine


Mass: 375.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.76 Å3/Da / Density % sol: 30.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1 mM zinc chloride, 22% PEG6000, 100 mM MES, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2→28.91 Å / Num. obs: 17144 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) all: 0.06 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 2 / Num. measured obs: 8360 / Num. unique obs: 1238 / CC1/2: 0.723 / Rpim(I) all: 0.537 / Rrim(I) all: 1.025 / Χ2: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CPY

6cpy


Resolution: 2→28.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.343 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25136 753 4.4 %RANDOM
Rwork0.20741 ---
obs0.20947 16362 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0 Å2
2---0.5 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 2→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 34 52 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0142062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171814
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6582799
X-RAY DIFFRACTIONr_angle_other_deg0.8881.6344204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87321.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80715319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.711514
X-RAY DIFFRACTIONr_chiral_restr0.0550.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
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_it3.0724.7191049
X-RAY DIFFRACTIONr_mcbond_other3.0724.7181048
X-RAY DIFFRACTIONr_mcangle_it4.2667.0661306
X-RAY DIFFRACTIONr_mcangle_other4.2657.0671307
X-RAY DIFFRACTIONr_scbond_it3.4284.981013
X-RAY DIFFRACTIONr_scbond_other3.4274.981013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9937.3631494
X-RAY DIFFRACTIONr_long_range_B_refined6.85157.0332360
X-RAY DIFFRACTIONr_long_range_B_other6.85257.0362361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 57 -
Rwork0.288 1176 -
obs--100 %

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