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- PDB-5e0z: Crystal Structure of PASTA Domains 3 and 4 of Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 5e0z
TitleCrystal Structure of PASTA Domains 3 and 4 of Mycobacterium tuberculosis Protein Kinase B
ComponentsSerine/threonine-protein kinase PknB
KeywordsTRANSFERASE / kinase / extracellular sensor domain / peptidoglycan binding / Structural Genomics / TB Structural Genomics Consortium / TBSGC
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 / peptidoglycan-based cell wall / negative regulation of protein binding ...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 / 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
Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Trypsin Inhibitor V; Chain A / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Trypsin Inhibitor V; Chain A / 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 / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPrigozhin, D.M. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM70962 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Genetic Analyses of the Mycobacterium tuberculosis Protein Kinase B Sensor Domain Identify a Potential Ligand-binding Site.
Authors: Prigozhin, D.M. / Papavinasasundaram, K.G. / Baer, C.E. / Murphy, K.C. / Moskaleva, A. / Chen, T.Y. / Alber, T. / Sassetti, C.M.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PknB


Theoretical massNumber of molelcules
Total (without water)14,3221
Polymers14,3221
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.466, 24.545, 64.874
Angle α, β, γ (deg.)90.000, 99.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PknB


Mass: 14321.913 Da / Num. of mol.: 1 / Fragment: UNP residues 491-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pknB, Rv0014c, MTCY10H4.14c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WI81, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M sodium acetate pH 4.5, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2→39.949 Å / Num. obs: 8592 / % possible obs: 97.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 20.87 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.072 / Net I/av σ(I): 10.619 / Net I/σ(I): 10 / Num. measured all: 19484
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.032.10.4794251.30693.8
2.03-2.072.20.4464011.41496.6
2.07-2.112.30.3854041.16597.1
2.11-2.152.30.3484421.25397.6
2.15-2.22.30.3054061.17796.4
2.2-2.252.30.274411.09197.8
2.25-2.312.40.2543921.19196.8
2.31-2.372.30.2154451.18497.8
2.37-2.442.30.1814351.03198
2.44-2.522.30.1684131.11697.9
2.52-2.612.30.1534271.04198.4
2.61-2.712.30.1184471.03397.8
2.71-2.842.30.1074061.07297.8
2.84-2.992.30.0714420.98198.2
2.99-3.172.30.0614360.99198
3.17-3.422.30.0444350.58298.2
3.42-3.762.30.0384280.97798.8
3.76-4.312.20.0314491.02698.5
4.31-5.432.20.0274350.89796
5.43-502.20.0274830.99399

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å39.95 Å
Translation2.5 Å39.95 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.2.4phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.949 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 809 9.96 %
Rwork0.1909 7317 -
obs0.1949 8126 91.87 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.61 Å2 / Biso mean: 24.8214 Å2 / Biso min: 8.65 Å2
Refinement stepCycle: final / Resolution: 2→39.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 0 100 1108
Biso mean---30.68 -
Num. residues----136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031049
X-RAY DIFFRACTIONf_angle_d0.7721434
X-RAY DIFFRACTIONf_chiral_restr0.023158
X-RAY DIFFRACTIONf_plane_restr0.003197
X-RAY DIFFRACTIONf_dihedral_angle_d12.428384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9996-2.12480.29591110.23431041115280
2.1248-2.28890.2691280.2281168129689
2.2889-2.51920.26461340.22041203133792
2.5192-2.88360.28021410.21431266140796
2.8836-3.63270.21041430.17051282142597
3.6327-39.95690.18811520.16521357150998

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