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- PDB-8pkr: Crystal structure of PknD-345, a repeat fragment from the M. tube... -

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Basic information

Entry
Database: PDB / ID: 8pkr
TitleCrystal structure of PknD-345, 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: 0.95 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: Computational design of the SAKe scaffold proteins
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3703
Polymers27,2782
Non-polymers921
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-24 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.701, 83.241, 83.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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


Mass: 13638.945 Da / Num. of mol.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.02 M Calcium chloride, 0.1 M Sodium acetate pH 4.6, 26% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.74999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.74999 Å / Relative weight: 1
ReflectionResolution: 0.95→41.73 Å / Num. obs: 142745 / % possible obs: 99.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 8.87 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.012 / Rrim(I) all: 0.045 / Net I/σ(I): 26.9 / Num. measured all: 1871882
Reflection shellResolution: 0.95→0.97 Å / % possible obs: 97.7 % / Redundancy: 13.4 % / Rmerge(I) obs: 1.223 / Num. measured all: 92378 / Num. unique obs: 6894 / CC1/2: 0.813 / Rpim(I) all: 0.342 / Rrim(I) all: 1.271 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→30.45 Å / SU ML: 0.0724 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.8557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1372 7091 4.97 %
Rwork0.1279 135549 -
obs0.1284 142640 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.86 Å2
Refinement stepCycle: LAST / Resolution: 0.95→30.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 6 235 2068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872024
X-RAY DIFFRACTIONf_angle_d1.12872811
X-RAY DIFFRACTIONf_chiral_restr0.0997339
X-RAY DIFFRACTIONf_plane_restr0.0089388
X-RAY DIFFRACTIONf_dihedral_angle_d12.2115717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.2212300.2234442X-RAY DIFFRACTION97.43
0.96-0.970.20852210.20594376X-RAY DIFFRACTION97.48
0.97-0.980.21372240.19014405X-RAY DIFFRACTION97.74
0.98-10.19642390.17924412X-RAY DIFFRACTION97.92
1-1.010.17592740.16184349X-RAY DIFFRACTION98.03
1.01-1.020.16432410.14244459X-RAY DIFFRACTION97.92
1.02-1.040.14172570.13414384X-RAY DIFFRACTION98.18
1.04-1.050.14082260.12954503X-RAY DIFFRACTION98.3
1.05-1.070.13842310.12464403X-RAY DIFFRACTION98.14
1.07-1.090.12642560.12344432X-RAY DIFFRACTION98.72
1.09-1.110.13572160.11584478X-RAY DIFFRACTION98.65
1.11-1.130.11052580.10534475X-RAY DIFFRACTION98.54
1.13-1.150.12582610.10264407X-RAY DIFFRACTION98.86
1.15-1.170.11062420.09744511X-RAY DIFFRACTION98.98
1.17-1.20.09712670.09874437X-RAY DIFFRACTION98.93
1.2-1.220.10711940.09694555X-RAY DIFFRACTION99.21
1.22-1.260.11552570.0984472X-RAY DIFFRACTION99.35
1.26-1.290.12072310.09994514X-RAY DIFFRACTION99.25
1.29-1.330.11072270.10424524X-RAY DIFFRACTION99.21
1.33-1.370.11262480.10614559X-RAY DIFFRACTION99.63
1.37-1.420.13492320.10484554X-RAY DIFFRACTION99.75
1.42-1.480.11842300.10864556X-RAY DIFFRACTION99.81
1.48-1.540.14752070.1084596X-RAY DIFFRACTION99.9
1.54-1.620.12661930.11114626X-RAY DIFFRACTION99.94
1.62-1.730.12562140.11874639X-RAY DIFFRACTION99.98
1.73-1.860.12092640.1254550X-RAY DIFFRACTION100
1.86-2.050.11432250.12194672X-RAY DIFFRACTION100
2.05-2.340.13122330.12674656X-RAY DIFFRACTION100
2.34-2.950.14772600.13944685X-RAY DIFFRACTION100
2.95-30.450.17092330.15664918X-RAY DIFFRACTION99.88

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