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- PDB-9eed: The Hanks-type kinase PknS from Xanthomonas citri bound to CHIR-124 -

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Basic information

Entry
Database: PDB / ID: 9eed
TitleThe Hanks-type kinase PknS from Xanthomonas citri bound to CHIR-124
ComponentsKinase domain protein
KeywordsTRANSFERASE / Ser-Thr Protein Kinase / Protein:Inhibitor complex
Function / homology
Function and homology information


protein serine/threonine kinase activity / ATP binding / membrane
Similarity search - Function
Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / 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. ...Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / 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
Chem-12C / Kinase domain protein
Similarity search - Component
Biological speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLima, L.P. / Alvarez-Martinez, C.E. / Massirer, K.B. / Counago, R.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: To Be Published
Title: The Hanks-type kinase PknS from Xanthomonas citri bound to CHIR-124
Authors: Lima, L.P. / Alvarez-Martinez, C.E. / Massirer, K.B. / Counago, R.M.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0223
Polymers39,5061
Non-polymers5162
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer based on gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-11 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.713, 76.713, 58.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Kinase domain protein


Mass: 39505.973 Da / Num. of mol.: 1 / Mutation: M164A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri (bacteria) / Gene: pknB, XAC3562_900036 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U5FKB2
#2: Chemical ChemComp-12C / 4-[(3S)-1-AZABICYCLO[2.2.2]OCT-3-YLAMINO]-3-(1H-BENZIMIDAZOL-2-YL)-6-CHLOROQUINOLIN-2(1H)-ONE


Mass: 419.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22ClN5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350; Lithium Sulfate 0.3M; 0.1M SBG pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo-stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2.1→29.65 Å / Num. obs: 20139 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 45.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.037 / Rrim(I) all: 0.085 / Χ2: 0.98 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.457 / Num. unique obs: 1657 / CC1/2: 0.639 / R split: 1.5 / Rpim(I) all: 1.539 / Rrim(I) all: 1.618 / Χ2: 0.86 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDS0.73data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.775 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23531 972 4.8 %RANDOM
Rwork0.19557 ---
obs0.19735 19138 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å2-0 Å2
2---0.45 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 5 67 2114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122105
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161955
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.8072873
X-RAY DIFFRACTIONr_angle_other_deg0.5671.7474467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.9397.2520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40810297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
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_it3.2284.0881089
X-RAY DIFFRACTIONr_mcbond_other3.2284.0881089
X-RAY DIFFRACTIONr_mcangle_it4.637.3311356
X-RAY DIFFRACTIONr_mcangle_other4.6297.3321357
X-RAY DIFFRACTIONr_scbond_it4.0444.4231016
X-RAY DIFFRACTIONr_scbond_other4.0094.4061013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8917.9261512
X-RAY DIFFRACTIONr_long_range_B_refined8.3540.872303
X-RAY DIFFRACTIONr_long_range_B_other8.35340.492299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 56 -
Rwork0.305 1387 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 27.0989 Å / Origin y: -5.9015 Å / Origin z: -4.5702 Å
111213212223313233
T0.022 Å2-0.0013 Å2-0.02 Å2-0.0626 Å2-0.0241 Å2--0.127 Å2
L3.2425 °2-0.047 °21.5684 °2-1.2189 °2-0.1901 °2--2.7798 °2
S0.106 Å °-0.0046 Å °-0.1859 Å °0.1079 Å °-0.004 Å °-0.3148 Å °0.0796 Å °0.3281 Å °-0.102 Å °

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