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- PDB-3f61: Crystal Structure of M. tuberculosis PknB Leu33Asp/Val222Asp doub... -

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Basic information

Entry
Database: PDB / ID: 3f61
TitleCrystal Structure of M. tuberculosis PknB Leu33Asp/Val222Asp double mutant in complex with ADP
ComponentsSerine/threonine-protein kinase pknB
KeywordsTRANSFERASE / protein kinase / PknB / Mycobacterium tuberculosis / Structural Genomics / PknB KD double mutant bound to ADP / TB Structural Genomics Consortium / TBSGC / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
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
ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase PknB / Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMieczkowski, C.A. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Embo J. / Year: 2008
Title: Auto-activation mechanism of the Mycobacterium tuberculosis PknB receptor Ser/Thr kinase.
Authors: Mieczkowski, C. / Iavarone, A.T. / Alber, T.
History
DepositionNov 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0616
Polymers33,5371
Non-polymers5245
Water3,315184
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.981, 51.542, 152.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase pknB


Mass: 33536.562 Da / Num. of mol.: 1 / Fragment: PknB kinase domain / Mutation: L33D, V222D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0017, MTCY10H4.14c, pknB, Rv0014c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon plus
References: UniProt: P0A5S4, UniProt: P9WI81*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3000, 3 mM ADP, 0.2 M NaF, 100mM Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11586 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2007
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11586 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29112 / % possible obs: 99.3 % / Redundancy: 8 % / Rmerge(I) obs: 0.056 / Χ2: 1.727 / Net I/σ(I): 48.607
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.76 / Num. unique all: 2689 / Χ2: 0.581 / % possible all: 93.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.77 Å
Translation2.5 Å37.77 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PknB Leu33Asp in complex with ATPgS

Resolution: 1.8→37.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.201 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.837 / SU B: 2.75 / SU ML: 0.084 / SU R Cruickshank DPI: 0.133 / SU Rfree: 0.122 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1477 5.1 %RANDOM
Rwork0.203 ---
obs0.205 27635 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.46 Å2 / Biso mean: 27.619 Å2 / Biso min: 15.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.229 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 31 184 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222192
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9833007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00223.53599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31615335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4141519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211708
X-RAY DIFFRACTIONr_mcbond_it0.8771.51393
X-RAY DIFFRACTIONr_mcangle_it1.55422259
X-RAY DIFFRACTIONr_scbond_it2.2533799
X-RAY DIFFRACTIONr_scangle_it3.7644.5744
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 107 -
Rwork0.31 1901 -
all-2008 -
obs--93.88 %

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