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- PDB-8pkq: Crystal structure of PknD-34, a repeat fragment from the M. tuber... -

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Basic information

Entry
Database: PDB / ID: 8pkq
TitleCrystal structure of PknD-34, a repeat fragment from the M. tuberculosis PknD beta-propeller
Componentsnon-specific serine/threonine protein kinase
KeywordsUNKNOWN FUNCTION / fragment / scaffold / beta propeller / globular / PknD
Function / homology
Function and homology information


regulation of cellular biosynthetic process / regulation of primary metabolic process / non-specific serine/threonine protein kinase / phosphorylation / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Protein kinase PknD, NHL repeat domain / NHL repeat profile. / NHL repeat / NHL repeat / Six-bladed beta-propeller, TolB-like / 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 kinase PknD, NHL repeat domain / NHL repeat profile. / NHL repeat / NHL repeat / Six-bladed beta-propeller, TolB-like / 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
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWouters, S.M.L.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S89918N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
CitationJournal: To Be Published
Title: Fragment-based assembly of a symmetric protein scaffold
Authors: Wouters, S.M.L. / Noguchi, H. / Voet, A.R.D.
History
DepositionJun 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: non-specific serine/threonine protein kinase
B: non-specific serine/threonine protein kinase
C: non-specific serine/threonine protein kinase


Theoretical massNumber of molelcules
Total (without water)27,3003
Polymers27,3003
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-31 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.351, 95.351, 69.829
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61

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Components

#1: Protein non-specific serine/threonine protein kinase


Mass: 9099.928 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: pknD_1, pknD_2, ERS007657_00042, ERS007663_00011, ERS007665_00696, ERS007720_00884, SAMEA2683035_02262
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A045HV41, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.68 Å / Num. obs: 36012 / % possible obs: 90.5 % / Redundancy: 17 % / Biso Wilson estimate: 20.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.025 / Rrim(I) all: 0.102 / Χ2: 1.03 / Net I/σ(I): 19.5 / Num. measured all: 613855
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.858 / Num. measured all: 39709 / Num. unique obs: 2105 / CC1/2: 0.925 / Rpim(I) all: 0.203 / Rrim(I) all: 0.882 / Χ2: 1.05 / Net I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.16 Å / SU ML: 0.1718 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 1711 4.76 %
Rwork0.1933 34253 -
obs0.1942 35964 90.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 142 1926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961817
X-RAY DIFFRACTIONf_angle_d1.18552493
X-RAY DIFFRACTIONf_chiral_restr0.0858300
X-RAY DIFFRACTIONf_plane_restr0.0128342
X-RAY DIFFRACTIONf_dihedral_angle_d12.2954641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.27591700.22093108X-RAY DIFFRACTION100
1.75-1.810.24121830.20763119X-RAY DIFFRACTION100
1.81-1.870.21261440.18013172X-RAY DIFFRACTION99.82
1.87-1.950.18031360.18653147X-RAY DIFFRACTION99.64
1.95-2.030.21961460.17943118X-RAY DIFFRACTION98.67
2.03-2.140.2041200.1853088X-RAY DIFFRACTION97.33
2.14-2.280.19571640.17292994X-RAY DIFFRACTION95.29
2.28-2.450.22741520.18792885X-RAY DIFFRACTION92.14
2.45-2.70.22371530.20852745X-RAY DIFFRACTION87.45
2.7-3.090.19971160.21552554X-RAY DIFFRACTION80.4
3.09-3.890.21391160.20322198X-RAY DIFFRACTION69.53
3.89-32.160.20751110.18242125X-RAY DIFFRACTION65.8

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