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- PDB-5m08: Crystal structure of Mycobacterium tuberculosis PknI kinase domai... -

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Basic information

Entry
Database: PDB / ID: 5m08
TitleCrystal structure of Mycobacterium tuberculosis PknI kinase domain, C20A_R136A double mutant
ComponentsSerine/threonine-protein kinase PknI
KeywordsSIGNALING PROTEIN / Tuberculosis / kinase / signalling
Function / homology
Function and homology information


regulation of growth rate / manganese ion binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PknI
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsLisa, M.N. / Wagner, T. / Alexandre, M. / Barilone, N. / Raynal, B. / Alzari, P.M. / Bellinzoni, M.
CitationJournal: FEBS J. / Year: 2017
Title: The crystal structure of PknI from Mycobacterium tuberculosis shows an inactive, pseudokinase-like conformation.
Authors: Lisa, M.N. / Wagner, T. / Alexandre, M. / Barilone, N. / Raynal, B. / Alzari, P.M. / Bellinzoni, M.
History
DepositionOct 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PknI
B: Serine/threonine-protein kinase PknI


Theoretical massNumber of molelcules
Total (without water)59,1052
Polymers59,1052
Non-polymers00
Water39622
1
A: Serine/threonine-protein kinase PknI


Theoretical massNumber of molelcules
Total (without water)29,5521
Polymers29,5521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase PknI


Theoretical massNumber of molelcules
Total (without water)29,5521
Polymers29,5521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.310, 109.310, 184.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Serine/threonine-protein kinase PknI


Mass: 29552.297 Da / Num. of mol.: 2 / Mutation: C20A,R136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pknI, Rv2914c, MTCY338.02c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WI69, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 4.65 Å3/Da / Density % sol: 73.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: NaCl 4.3 M, 0.1 M Hepes-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.03→48.88 Å / Num. obs: 22374 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 96.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.7
Reflection shellResolution: 3.03→3.21 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / CC1/2: 0.905 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5M07

5m07


Resolution: 3.03→48.88 Å / Cor.coef. Fo:Fc: 0.9356 / Cor.coef. Fo:Fc free: 0.9189 / SU R Cruickshank DPI: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 1132 5.06 %RANDOM
Rwork0.1837 ---
obs0.1849 22374 99.85 %-
Displacement parametersBiso mean: 87.18 Å2
Baniso -1Baniso -2Baniso -3
1--10.4345 Å20 Å20 Å2
2---10.4345 Å20 Å2
3---20.8691 Å2
Refine analyzeLuzzati coordinate error obs: 0.374 Å
Refinement stepCycle: 1 / Resolution: 3.03→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3710 0 0 22 3732
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013798HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035181HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1677SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes584HARMONIC5
X-RAY DIFFRACTIONt_it3798HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion2.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion491SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4225SEMIHARMONIC4
LS refinement shellResolution: 3.03→3.18 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2713 144 4.96 %
Rwork0.2712 2760 -
all0.2712 2904 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.45682.0718-2.09274.7679-0.55323.4101-0.20420.35740.7253-0.12550.16620.5703-0.6201-0.09270.038-0.0004-0.1448-0.0218-0.057-0.0251-0.1185-50.468211.7377-14.8123
23.8208-0.9517-2.34.56541.40744.8764-0.25040.0475-0.50910.1318-0.16180.56780.5054-0.02390.4122-0.1802-0.1060.1871-0.1823-0.0548-0.0829-50.6272-12.7611-16.7938
32.39063.4469-0.66015.9147-3.32816.0358-0.23250.2149-0.5499-0.3912-0.2032-0.81370.59550.59110.4357-0.0993-0.08930.0547-0.1298-0.0358-0.1226-19.143325.0971-13.1122
44.27672.25461.18793.97821.86785.13630.0559-0.4944-0.00820.3882-0.17970.10220.7374-0.3590.1238-0.0004-0.15390.029-0.1381-0.0418-0.1866-26.741525.29029.7175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|94 }
2X-RAY DIFFRACTION2{ A|95 - A|256 }
3X-RAY DIFFRACTION3{ B|1 - B|94 }
4X-RAY DIFFRACTION4{ B|95 - B|256 }

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