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- PDB-4x3f: Crystal structure of the intracellular domain of the M. tuberculo... -

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Basic information

Entry
Database: PDB / ID: 4x3f
TitleCrystal structure of the intracellular domain of the M. tuberculosis Ser/Thr kinase PknA
Components(Serine/threonine-protein kinase PknA) x 3
KeywordsTRANSFERASE / Kinase / autoinhibition / phosphorylation
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / negative regulation of lipid biosynthetic process / regulation of fatty acid metabolic process / negative regulation of fatty acid biosynthetic process / regulation of cell shape / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / extracellular region ...peptidyl-threonine autophosphorylation / negative regulation of lipid biosynthetic process / regulation of fatty acid metabolic process / negative regulation of fatty acid biosynthetic process / regulation of cell shape / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 domain profile. / Protein kinase domain ...Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PknA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWagner, T. / Wehenkel, A. / Alzari, P.M. / Bellinzoni, M.
CitationJournal: Proteins / Year: 2015
Title: The crystal structure of the catalytic domain of the ser/thr kinase PknA from M. tuberculosis shows an Src-like autoinhibited conformation.
Authors: Wagner, T. / Alexandre, M. / Duran, R. / Barilone, N. / Wehenkel, A. / Alzari, P.M. / Bellinzoni, M.
History
DepositionNov 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PknA
B: Serine/threonine-protein kinase PknA
C: Serine/threonine-protein kinase PknA


Theoretical massNumber of molelcules
Total (without water)107,8143
Polymers107,8143
Non-polymers00
Water18010
1
A: Serine/threonine-protein kinase PknA


Theoretical massNumber of molelcules
Total (without water)36,0181
Polymers36,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PknA


Theoretical massNumber of molelcules
Total (without water)35,9381
Polymers35,9381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase PknA


Theoretical massNumber of molelcules
Total (without water)35,8581
Polymers35,8581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.310, 150.180, 96.540
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA3 - 2884 - 289
21PROPROBB3 - 2884 - 289
12PROPROAA3 - 2894 - 290
22PROPROCC3 - 2894 - 290
13SERSERBB2 - 2893 - 290
23SERSERCC2 - 2893 - 290

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Serine/threonine-protein kinase PknA


Mass: 36017.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: pknA, Rv0015c, MTCY10H4.15c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WI83, non-specific serine/threonine protein kinase
#2: Protein Serine/threonine-protein kinase PknA


Mass: 35937.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: pknA, Rv0015c, MTCY10H4.15c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WI83, non-specific serine/threonine protein kinase
#3: Protein Serine/threonine-protein kinase PknA


Mass: 35857.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: pknA, Rv0015c, MTCY10H4.15c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WI83, non-specific serine/threonine protein kinase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 4.3 M NaCl, 0.1 M Hepes-Na pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→43.6 Å / Num. obs: 31961 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.197 / Mean I/σ(I) obs: 1.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1o6y

1o6y


Resolution: 2.9→43.56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 46.23 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R: 0.636 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24302 1606 5 %RANDOM
Rwork0.21912 ---
obs0.22033 30353 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.212 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å20 Å21.5 Å2
2---0.5 Å20 Å2
3---3.6 Å2
Refinement stepCycle: 1 / Resolution: 2.9→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6017 0 0 10 6027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196151
X-RAY DIFFRACTIONr_bond_other_d0.0040.025831
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9888413
X-RAY DIFFRACTIONr_angle_other_deg1.144313324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1885824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04722.297222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55515854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3391554
X-RAY DIFFRACTIONr_chiral_restr0.0630.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217062
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021322
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3775.193317
X-RAY DIFFRACTIONr_mcbond_other3.3695.193316
X-RAY DIFFRACTIONr_mcangle_it5.2147.7744134
X-RAY DIFFRACTIONr_mcangle_other5.2147.7754135
X-RAY DIFFRACTIONr_scbond_it4.0775.4662834
X-RAY DIFFRACTIONr_scbond_other4.0765.4672835
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2918.0644280
X-RAY DIFFRACTIONr_long_range_B_refined7.87840.3786079
X-RAY DIFFRACTIONr_long_range_B_other7.87840.3856080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A145840.08
12B145840.08
21A144450.08
22C144450.08
31B149680.07
32C149680.07
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 129 -
Rwork0.356 2201 -
obs--98.23 %
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)
15.675-2.7243-1.33035.5240.50483.6420.43530.70450.169-0.611-0.4440.3439-0.4169-0.2280.00870.4387-0.0572-0.09630.505-0.07130.168914.9652.624-6.509
26.0762-0.5157-0.94572.49050.69862.84320.0178-0.0015-0.2693-0.0515-0.10970.13580.1754-0.09490.09190.437-0.0860.09050.2454-0.05960.19536.754-8.5313.976
37.7087-0.46880.89955.2329-1.32367.8457-0.30940.3587-0.18690.19450.3617-0.06330.3139-0.5388-0.05230.51230.10630.21230.1524-0.06450.43490.875-12.443-34.273
42.8587-2.08672.13554.5744-2.29923.9474-0.04520.10570.08730.0706-0.0142-0.3279-0.22320.03040.05940.39420.10380.13890.0621-0.08310.568623.868-27.03-34.272
55.4525-0.5254-0.65076.8939-0.83496.44580.11430.0107-0.0390.0374-0.1169-0.18050.4745-0.31330.00260.39680.20540.15350.2236-0.02090.3855-10.2270.619-22.663
64.0007-0.86110.33925.5958-2.49844.1202-0.1441-0.23290.31160.38350.0226-0.1964-0.10110.0950.12150.40570.14180.07460.0979-0.10030.4568-15.80226.367-17.547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 98
2X-RAY DIFFRACTION2A99 - 289
3X-RAY DIFFRACTION3B0 - 98
4X-RAY DIFFRACTION4B99 - 289
5X-RAY DIFFRACTION5C2 - 98
6X-RAY DIFFRACTION6C99 - 289

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