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

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Basic information

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


regulation of cellular biosynthetic process / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / protein phosphorylation / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
PASTA domain / PASTA / PASTA domain / PASTA domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 ...PASTA domain / PASTA / PASTA domain / PASTA domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinases ATP-binding region signature. / Protein kinase, ATP binding site / 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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsEchols, N. / Lombana, T.N. / Thomsen, N.D. / Ng, H.-L. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2010
Title: Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr 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

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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)34,0993
Polymers33,5211
Non-polymers5782
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.191, 50.633, 132.762
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 / Serine/threonine-specific protein kinase


Mass: 33520.605 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 1 to 308) / Mutation: L33D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (unknown) / Strain: H37Rv / Gene: MRA_0016, pknB, PknB (Rv0014c) / Production host: Escherichia coli (E. coli) / References: UniProt: A5TY84
#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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 100mM Tris pH 8.5, 200mM ammonium sulfate, 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: 1.8927 / Wavelength: 1.8927 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8927 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 6052 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1mru
Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.847 / SU B: 33.394 / SU ML: 0.369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27658 338 5.3 %RANDOM
Rwork0.21057 ---
obs0.21379 6052 100 %-
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: 41.378 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2---2.59 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 32 50 2063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222051
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg11.9892812
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7365266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41324.52484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98115292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4751511
X-RAY DIFFRACTIONr_chiral_restr0.0590.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021573
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2919
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21403
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 24 -
Rwork0.313 421 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.83340.26980.00491.8256-1.49291.2849-0.08270.04760.163-0.02820.1245-0.045-0.122-0.1778-0.0419-0.06550.0157-0.04490.00080.01810.0418.532944.7929.9905
2281.6374-331.74380.8863484.355104.7403450.6895-7.74529.5593-1.15960.4149-2.2477-9.2893-0.05176.94839.99280.0550.27760.0231-0.0001-0.08310.002814.861635.6257-6.7503
31.0501-0.56710.340.82720.03870.62940.0682-0.0205-0.0214-0.0424-0.0193-0.02620.04420.029-0.04880.0039-0.0141-0.0636-0.00220.0207-0.003933.162226.081323.0755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 47
2X-RAY DIFFRACTION1A67 - 96
3X-RAY DIFFRACTION2A48
4X-RAY DIFFRACTION3A97 - 155
5X-RAY DIFFRACTION3A195 - 285

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