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- PDB-1o6y: Catalytic domain of PknB kinase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1o6y
TitleCatalytic domain of PknB kinase from Mycobacterium tuberculosis
ComponentsSERINE/THREONINE-PROTEIN KINASE PKNB
KeywordsTRANSFERASE / SERINE/THREONINE PROTEIN KINASE / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TB / TBSGC
Function / homology
Function and homology information


negative regulation of growth rate / negative regulation of fatty acid biosynthetic process / acetyltransferase activator activity / response to host immune response / membrane => GO:0016020 / peptidoglycan biosynthetic process / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / regulation of cell shape / manganese ion binding ...negative regulation of growth rate / negative regulation of fatty acid biosynthetic process / acetyltransferase activator activity / response to host immune response / membrane => GO:0016020 / peptidoglycan biosynthetic process / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / regulation of cell shape / manganese ion binding / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Serine/threonine-protein kinase PknB / Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOrtiz-Lombardia, M. / Pompeo, F. / Boitel, B. / Alzari, P.M. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of the Catalytic Domain of the Pknb Serine/Threonine Kinase from Mycobacterium Tuberculosis
Authors: Ortiz-Lombardia, M. / Pompeo, F. / Boitel, B. / Alzari, P.M.
History
DepositionOct 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 24, 2017Group: Structure summary
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.4Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: SERINE/THREONINE-PROTEIN KINASE PKNB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0124
Polymers32,4591
Non-polymers5543
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.607, 122.088, 46.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE PKNB / PKNB


Mass: 32458.506 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-279
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: INSTITUT PASTEUR COLLECTION / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A5S4, UniProt: P9WI81*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES IN THE N-TERMINAL TAG (1-22) ARE DISORDERED. SIXTEEN RESIDUES (164-179) IN THE ACTIVATION ...RESIDUES IN THE N-TERMINAL TAG (1-22) ARE DISORDERED. SIXTEEN RESIDUES (164-179) IN THE ACTIVATION LOOP ARE ALSO DISORDERED.

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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: 2.22 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN CRYSTALLIZED FROM 27% PEG 400, 4% 1,3-BUTANEDIOL, 100 MM HEPES, PH 7.5, 30 MM MGCL2 AT 19 DEGREES C
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
330 mM1reservoirMgCl2
4150000 mMAMP-PCP1reservoir
527 %PEG4001reservoir
64 %1,3-butanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→60.86 Å / Num. obs: 17152 / % possible obs: 99.8 % / Redundancy: 8 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.3 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 61 Å / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.64

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PHK

1phk


Resolution: 2.2→61 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.608 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 848 5 %RANDOM
Rwork0.1909 ---
obs0.1927 16292 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.841 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---3.59 Å20 Å2
3---4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 33 85 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212026
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9722767
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1925258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1150.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021541
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2840
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.791.51299
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40622090
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5333727
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7634.5677
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 59
Rwork0.22 1195
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)
13.8276-0.226-1.34765.3644-0.17984.6566-0.09760.01330.27790.0536-0.04221.0543-0.3597-0.7030.13980.11440.0375-0.03410.1231-0.06210.282275.106471.597725.0741
25.74361.2839-1.07524.67180.02423.12340.1102-0.09030.3283-0.0189-0.0667-0.0839-0.12830.1966-0.04350.07240.03850.01340.06750.02510.014899.291681.350717.413
314.0382-16.644326.042440.4748-30.566225.46520.0025-0.47270.60870.45720.4664-0.5314-0.6783-0.7214-0.46880.03980.0676-0.02450.1537-0.04660.122683.008977.943625.8829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 97
2X-RAY DIFFRACTION2A98 - 278
3X-RAY DIFFRACTION3A1279
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.623

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