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- PDB-5m07: Crystal structure of Mycobacterium tuberculosis PknI kinase domai... -

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Basic information

Entry
Database: PDB / ID: 5m07
TitleCrystal structure of Mycobacterium tuberculosis PknI kinase domain, C20A mutant
ComponentsSerine/threonine-protein kinase PknI
KeywordsSIGNALING PROTEIN / Tuberculosis / kinase / signalling / transferase
Function / homology
Function and homology information


regulation of growth rate / peptidyl-threonine phosphorylation / manganese ion binding / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...regulation of growth rate / peptidyl-threonine phosphorylation / manganese ion binding / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PknI
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLisa, M.N. / Wagner, T. / Alexandre, M. / Barilone, N. / Raynal, B. / Alzari, P.M. / Bellinzoni, M.
CitationJournal: FEBS J. / Year: 2017
Title: The crystal structure of PknI from Mycobacterium tuberculosis shows an inactive, pseudokinase-like conformation.
Authors: Lisa, M.N. / Wagner, T. / Alexandre, M. / Barilone, N. / Raynal, B. / Alzari, P.M. / Bellinzoni, M.
History
DepositionOct 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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 PknI
B: Serine/threonine-protein kinase PknI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3234
Polymers59,2772
Non-polymers462
Water2,774154
1
A: Serine/threonine-protein kinase PknI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6612
Polymers29,6381
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PknI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6612
Polymers29,6381
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.304, 108.304, 185.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Serine/threonine-protein kinase PknI


Mass: 29638.414 Da / Num. of mol.: 2 / Mutation: C20A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: pknI, Rv2914c, MTCY338.02c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WI69, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 4.59 Å3/Da / Density % sol: 73.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 3.5 M NaCl, 0.08 M Hepes-Na pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→48.44 Å / Num. obs: 38990 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 89.02 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Net I/σ(I): 29.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 13 % / Rmerge(I) obs: 1.836 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.794 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5M06

5m06


Resolution: 2.5→36.14 Å / Cor.coef. Fo:Fc: 0.9465 / Cor.coef. Fo:Fc free: 0.9333 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 1958 5.03 %RANDOM
Rwork0.2085 ---
obs0.2098 38927 99.99 %-
Displacement parametersBiso mean: 85.32 Å2
Baniso -1Baniso -2Baniso -3
1--6.2927 Å20 Å20 Å2
2---6.2927 Å20 Å2
3---12.5853 Å2
Refine analyzeLuzzati coordinate error obs: 0.366 Å
Refinement stepCycle: 1 / Resolution: 2.5→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 2 154 3870
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013800HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.015177HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1690SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes580HARMONIC5
X-RAY DIFFRACTIONt_it3800HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion2.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion485SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4221SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3529 131 4.67 %
Rwork0.2724 2673 -
all0.276 2804 -
obs--100 %
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)
14.25332.0216-0.6124.8413-1.32073.0742-0.22570.23550.5682-0.02520.1830.6324-0.5422-0.21880.0428-0.1305-0.110.0248-0.1399-0.0511-0.2042-50.118911.496-14.7262
23.3187-1.5528-1.88652.82450.94993.8363-0.2103-0.0067-0.48660.1346-0.09050.43670.508-0.09140.3008-0.2332-0.10830.162-0.2111-0.0601-0.2081-50.5332-12.7792-17.1542
31.86913.4991-0.34985.2735-3.00075.2312-0.26560.16-0.6573-0.3957-0.1498-0.79650.49520.55250.4154-0.0934-0.04710.0751-0.178-0.0214-0.1709-18.899725.027-13.2488
42.72290.76351.31692.86521.65434.54560.0636-0.47290.00810.429-0.12490.05980.7181-0.28530.0613-0.0738-0.12340.0138-0.21460.003-0.3068-26.26424.84629.5932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|94 }
2X-RAY DIFFRACTION2{ A|95 - A|256 }
3X-RAY DIFFRACTION3{ B|1 - B|94 }
4X-RAY DIFFRACTION4{ B|95 - B|256 }

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