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- PDB-3oro: Mycobacterium tuberculosis PknB kinase domain L33D mutant (crysta... -

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Basic information

Entry
Database: PDB / ID: 3oro
TitleMycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 4)
ComponentsSerine/threonine protein kinase
KeywordsTRANSFERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Kinase domain / Signal transduction
Function / homology
Function and homology information


negative regulation of growth rate / regulation of primary metabolic process / 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 / peptidoglycan-based cell wall ...negative regulation of growth rate / regulation of primary metabolic process / 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 / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / regulation of cell shape / protein autophosphorylation / 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 / 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
PHOSPHOTHIOPHOSPHORIC 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: 1.9 Å
AuthorsGood, M.C. / Echols, N. / Lombana, T.N. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2010
Title: Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB.
Authors: Lombana, T.N. / Echols, N. / Good, M.C. / Thomsen, N.D. / Ng, H.L. / Greenstein, A.E. / Falick, A.M. / King, D.S. / Alber, T.
History
DepositionSep 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2513
Polymers33,5211
Non-polymers7312
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.598, 51.423, 135.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine protein kinase


Mass: 33520.605 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 1 to 308)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MRA_0016, pknB, PknB (Rv0014c) / Production host: Escherichia coli (E. coli) / References: UniProt: A5TY84, UniProt: P9WI81*PLUS
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1M Sodium Citrate, 100mM CHES 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: 1.107 / Wavelength: 1.107 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 1, 2003
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1071
21.1071
ReflectionResolution: 1.9→20 Å / Num. obs: 21540 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 5.2 / % possible all: 94.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
EPMRphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1mru

1mru


Resolution: 1.9→17.46 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.554 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22758 1161 5.1 %RANDOM
Rwork0.19296 ---
obs0.19474 21540 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 44 205 2297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222148
X-RAY DIFFRACTIONr_bond_other_d0.0010.021979
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9892936
X-RAY DIFFRACTIONr_angle_other_deg0.7443.0014558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0465272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98822.93592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2815320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8751520
X-RAY DIFFRACTIONr_chiral_restr0.1230.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
X-RAY DIFFRACTIONr_nbd_refined0.2030.2417
X-RAY DIFFRACTIONr_nbd_other0.1670.21950
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21058
X-RAY DIFFRACTIONr_nbtor_other0.080.21253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.51757
X-RAY DIFFRACTIONr_mcbond_other0.1011.5547
X-RAY DIFFRACTIONr_mcangle_it0.80422197
X-RAY DIFFRACTIONr_scbond_it1.4153882
X-RAY DIFFRACTIONr_scangle_it2.0564.5739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 67 -
Rwork0.247 1434 -
obs--91.41 %
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)
10.95460.4188-1.01386.6997-2.11091.7953-0.11410.0786-0.3498-0.2609-0.1375-0.07710.1587-0.040.2515-0.0419-0.03060.0446-0.1301-0.00530.052841.458426.16187.2414
25.608-1.4501-1.60012.70640.67682.9244-0.2821-0.2154-0.5574-0.22060.1998-0.14960.27380.33570.0822-0.03250.03840.059-0.09510.0831-0.001145.043328.586513.0883
341.609454.1779-40.582570.5428-52.840839.5809-1.63040.3155-0.2347-1.86530.1448-3.93342.0490.48761.48570.18470.1180.14950.0607-0.12610.115952.134137.3022-4.3586
45.32360.2044-1.75561.66220.1652.3259-0.141-0.5234-0.3349-0.0907-0.07740.05320.06650.26080.2184-0.0695-0.0043-0.001-0.04560.0716-0.083830.678438.799221.0951
53.58860.9405-1.62121.7543-0.68341.93530.3768-0.56050.39550.1831-0.21170.1953-0.34160.3037-0.1651-0.029-0.1240.049-0.0342-0.0896-0.066128.057552.488425.2206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 47
2X-RAY DIFFRACTION2A67 - 96
3X-RAY DIFFRACTION3A48
4X-RAY DIFFRACTION4A97 - 155
5X-RAY DIFFRACTION5A195 - 285

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