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- PDB-4esq: Crystal structure of the extracellular domain of PknH from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 4esq
TitleCrystal structure of the extracellular domain of PknH from Mycobacterium tuberculosis
ComponentsSerine/threonine protein kinase
KeywordsTRANSFERASE / Receptor Kinase / Membrane
Function / homology
Function and homology information


regulation of primary metabolic process / regulation of lipid biosynthetic process / negative regulation of growth / negative regulation of catalytic activity / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan-based cell wall / protein autophosphorylation / non-specific serine/threonine protein kinase ...regulation of primary metabolic process / regulation of lipid biosynthetic process / negative regulation of growth / negative regulation of catalytic activity / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan-based cell wall / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / ATP binding / plasma membrane
Similarity search - Function
PknH-like extracellular domain / PknH-like extracellular domain / PknH-like extracellular domain superfamily / PknH-like extracellular domain / Protein Transport Mog1p; Chain A / 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 ...PknH-like extracellular domain / PknH-like extracellular domain / PknH-like extracellular domain superfamily / PknH-like extracellular domain / Protein Transport Mog1p; Chain A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TERBIUM(III) ION / non-specific serine/threonine protein kinase / Serine/threonine-protein kinase PknH
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsCavazos, A. / Prigozhin, D.M. / Alber, T.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structure of the sensor domain of Mycobacterium tuberculosis PknH receptor kinase reveals a conserved binding cleft.
Authors: Cavazos, A. / Prigozhin, D.M. / Alber, T.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1894
Polymers20,6621
Non-polymers5273
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.455, 35.923, 49.308
Angle α, β, γ (deg.)90.000, 98.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine protein kinase


Mass: 20661.994 Da / Num. of mol.: 1 / Fragment: unp residues 83332-83523
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: pknH, Rv1266c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: A5U1W4, UniProt: P9WI71*PLUS
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG 3350, 50mM terbium nitrate, pH 5.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2011
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 17.44 / Number: 69365 / Rmerge(I) obs: 0.061 / Χ2: 1.01 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 18089 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665099.710.040.983.8
2.913.6699.910.0550.963.8
2.542.9199.710.0611.0813.9
2.312.5499.610.0681.0263.9
2.142.3199.110.0731.0773.9
2.022.1498.910.0861.0643.9
1.912.0298.210.1081.013.9
1.831.9197.710.1481.0053.8
1.761.8397.510.1981.0173.8
1.71.7698.110.2530.9273.8
ReflectionResolution: 1.7→50 Å / Num. obs: 34200 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.061 / Χ2: 1.015 / Net I/σ(I): 17.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.80.25317600.927198.1
1.76-1.833.80.19817681.017197.5
1.83-1.913.80.14817861.005197.7
1.91-2.023.90.10817601.01198.2
2.02-2.143.90.08618171.064198.9
2.14-2.313.90.07317801.077199.1
2.31-2.543.90.06818411.026199.6
2.54-2.913.90.06118271.081199.7
2.91-3.663.80.05518530.96199.9
3.66-503.80.0418970.98199.7

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.69 / FOM acentric: 0.71 / FOM centric: 0.51 / Reflection: 8491 / Reflection acentric: 7763 / Reflection centric: 728
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.9-6.30.850.880.6711471008139
3.1-3.90.830.850.6514391310129
2.8-3.10.720.740.4814241314110
2.4-2.80.60.620.3425172354163
2.2-2.40.510.520.251568147197

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.15phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→48.784 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.39 / σ(F): 1.35 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 878 4.92 %RANDOM
Rwork0.163 ---
obs0.1647 34190 96.67 %-
all-34190 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.934 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 55.6 Å2 / Biso mean: 18.0416 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.7031 Å2-0 Å2-2.6978 Å2
2---0.8074 Å20 Å2
3---2.5105 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 16 221 1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131522
X-RAY DIFFRACTIONf_angle_d0.962084
X-RAY DIFFRACTIONf_chiral_restr0.06236
X-RAY DIFFRACTIONf_plane_restr0.004270
X-RAY DIFFRACTIONf_dihedral_angle_d18.747556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7005-1.75050.23681370.22612595273294
1.7505-1.8070.26811470.19852635278294
1.807-1.87160.21651220.18422686280896
1.8716-1.94650.21691480.16352663281196
1.9465-2.03510.21321440.15312710285496
2.0351-2.14240.1731410.15122707284896
2.1424-2.27670.21731450.15232735288097
2.2767-2.45240.19671330.17032720285398
2.4524-2.69920.22811420.17812756289898
2.6992-3.08970.18991440.17392755289998
3.0897-3.89250.17211330.15382775290898
3.8925-48.80420.17871470.14612770291799

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