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- PDB-2fum: Catalytic domain of protein kinase PknB from Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 2fum
TitleCatalytic domain of protein kinase PknB from Mycobacterium tuberculosis in complex with mitoxantrone
ComponentsProbable serine/threonine-protein kinase pknB
KeywordsTRANSFERASE / PROTEIN KINASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of growth rate / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall ...negative regulation of growth rate / acetyltransferase activator activity / negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / response to host immune response / positive regulation of catalytic activity / positive regulation of DNA binding / peptidoglycan biosynthetic process / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / regulation of cell shape / protein autophosphorylation / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MIX / Serine/threonine-protein kinase PknB / Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsWehenkel, A. / Alzari, P.M.
CitationJournal: Febs Lett. / Year: 2006
Title: The structure of PknB in complex with mitoxantrone, an ATP-competitive inhibitor, suggests a mode of protein kinase regulation in mycobacteria
Authors: Wehenkel, A. / Fernandez, P. / Bellinzoni, M. / Catherinot, V. / Barilone, N. / Labesse, G. / Jackson, M. / Alzari, P.M.
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable serine/threonine-protein kinase pknB
B: Probable serine/threonine-protein kinase pknB
C: Probable serine/threonine-protein kinase pknB
D: Probable serine/threonine-protein kinase pknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6128
Polymers129,8344
Non-polymers1,7784
Water0
1
A: Probable serine/threonine-protein kinase pknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9032
Polymers32,4591
Non-polymers4441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable serine/threonine-protein kinase pknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9032
Polymers32,4591
Non-polymers4441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable serine/threonine-protein kinase pknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9032
Polymers32,4591
Non-polymers4441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable serine/threonine-protein kinase pknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9032
Polymers32,4591
Non-polymers4441
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.863, 116.863, 260.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12C
22D
32C
42D

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRILEILEAA3 - 16323 - 183
211THRTHRILEILEBB3 - 16323 - 183
321GLYGLYHISHISAA178 - 277198 - 297
421GLYGLYHISHISBB178 - 277198 - 297
112THRTHRPHEPHECC3 - 15723 - 177
212THRTHRPHEPHEDD3 - 15723 - 177
322ALAALAHISHISCC180 - 277200 - 297
422ALAALAHISHISDD180 - 277200 - 297

NCS ensembles :
ID
1
2

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Components

#1: Protein
Probable serine/threonine-protein kinase pknB / PKNB SER/THR KINASE


Mass: 32458.506 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Gene: pknB / Plasmid: PET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P0A5S4, UniProt: P9WI81*PLUS, EC: 2.7.1.37
#2: Chemical
ChemComp-MIX / 1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)-9,10-ANTHRACENEDIONE / MITOXANTRONE / 1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)ANTHRA-9,10-QUINONE / Mitoxantrone


Mass: 444.481 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H28N4O6 / Comment: antineoplastic*YM

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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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.2M NaAcetate 50mM NaCacodylate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2005
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.89→69.84 Å / Num. all: 28195 / Num. obs: 28195 / % possible obs: 63.47 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.89→3.21 Å / % possible all: 16

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O6Y

1o6y


Resolution: 2.89→69.84 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 53.161 / SU ML: 0.412 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE DATA IS HIGHLY ANISOTROPIC (2.89 A RESOLUTION LIMIT ALONG THE c* AXIS, BUT ONLY 3.5 A ALONG THE a* AND b* AXES), ACCOUNTING FOR THE POOR DATA COMPLETENESS AT THE HIGHER RESOLUTION SHELLS ...Details: THE DATA IS HIGHLY ANISOTROPIC (2.89 A RESOLUTION LIMIT ALONG THE c* AXIS, BUT ONLY 3.5 A ALONG THE a* AND b* AXES), ACCOUNTING FOR THE POOR DATA COMPLETENESS AT THE HIGHER RESOLUTION SHELLS (DATA IS 99% COMPLETE AT 3.49 A, 45% IN THE 3.49-3.21 A SHELL, AND ONLY 16% IN THE 3.21-2.89 A SHELL.
RfactorNum. reflection% reflectionSelection details
Rfree0.27798 1426 5.1 %RANDOM
Rwork0.21784 ---
obs0.22097 26685 68.13 %-
all-26685 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.784 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å20 Å2
2--3.91 Å20 Å2
3----7.82 Å2
Refinement stepCycle: LAST / Resolution: 2.89→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7870 0 128 0 7998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228171
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9811143
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21251029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06923.579366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.322151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6951566
X-RAY DIFFRACTIONr_chiral_restr0.1270.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026315
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2660.24512
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.25666
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2384
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3191.55272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56628336
X-RAY DIFFRACTIONr_scbond_it1.1433497
X-RAY DIFFRACTIONr_scangle_it2.0744.52807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1028tight positional0.090.05
2C1000tight positional0.070.05
1A925medium positional0.680.5
2C898medium positional0.630.5
1A1028tight thermal0.10.5
2C1000tight thermal0.080.5
1A925medium thermal0.622
2C898medium thermal0.52
LS refinement shellResolution: 2.891→2.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 17 -
Rwork0.341 217 -
obs--7.81 %
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)
14.4687-1.65040.12886.2814-1.40138.5972-0.04720.0765-0.27870.56860.1803-0.64010.17631.1117-0.1330.13440.14840.01840.1291-0.0342-0.401867.0125-6.545-29.4674
25.87020.9899-0.72764.22980.30969.2680.465-0.2260.4728-0.0149-0.34190.4071-0.4227-1.0215-0.1232-0.02750.18580.08490.00820.0606-0.295544.79114.5138-19.3964
33.4415-0.6644-2.5188.71881.83988.97660.08860.3725-0.3847-0.38790.2819-0.64410.39041.0653-0.37040.1330.2421-0.06330.1710.0686-0.40564.8508-9.9255-50.3222
42.57920.81570.50787.0844-0.93199.0768-0.021-0.18850.2804-0.07560.30420.4925-1.4792-0.4772-0.28320.20170.31960.0557-0.00420.1167-0.27950.841310.5132-61.176
513.0911-2.77481.97195.6346-1.53688.1272-0.2334-1.29270.48170.96140.2270.1945-0.9569-0.08040.00640.55810.20310.0817-0.22360.08670.141482.2391-52.4819-16.0674
63.2682-2.9604-0.7258.4385-0.90373.82360.30240.395-0.313-0.5721-0.40890.3902-0.1276-0.35180.10650.41840.2856-0.09710.0340.0270.05767.1133-39.6418-35.1497
75.833-1.2247-0.79788.2543.037810.7647-0.2015-1.2362-1.62270.79150.12890.68331.3560.0420.07260.49060.03820.10940.12930.23880.72378.8837-73.543-17.9286
83.56490.4624-2.29314.94951.29097.3434-0.17030.6221-0.4317-0.8218-0.09930.8760.162-0.73980.26950.74650.0775-0.3271-0.003-0.08920.474278.5643-79.9137-44.4222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 9623 - 116
2X-RAY DIFFRACTION2AA97 - 277117 - 297
3X-RAY DIFFRACTION3BB3 - 9623 - 116
4X-RAY DIFFRACTION4BB97 - 278117 - 298
5X-RAY DIFFRACTION5CC3 - 9623 - 116
6X-RAY DIFFRACTION6CC97 - 278117 - 298
7X-RAY DIFFRACTION7DD3 - 9623 - 116
8X-RAY DIFFRACTION8DD97 - 277117 - 297

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