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- PDB-5e12: Crystal Structure of PASTA Domains 2, 3 and 4 of Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 5000000000000
TitleCrystal Structure of PASTA Domains 2, 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
CITRATE ANION / Serine/threonine-protein kinase PknB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.208 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 / database_2
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
B: Serine/threonine-protein kinase PknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9113
Polymers42,7222
Non-polymers1891
Water2,540141
1
A: Serine/threonine-protein kinase PknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5502
Polymers21,3611
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PknB


Theoretical massNumber of molelcules
Total (without water)21,3611
Polymers21,3611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.297, 24.524, 73.370
Angle α, β, γ (deg.)90.000, 89.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PknB


Mass: 21360.895 Da / Num. of mol.: 2 / Fragment: UNP residues 423-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (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: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M citrate pH 3.5, 25% PEG 3350

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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: Feb 19, 2011
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: 2.2→41.902 Å / Num. obs: 18775 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 25.98 Å2 / Rmerge(I) obs: 0.138 / Χ2: 1.154 / Net I/av σ(I): 7.79 / Net I/σ(I): 7.8 / Num. measured all: 74634
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.2840.65517991.419100
2.28-2.3740.59718531.404100
2.37-2.4840.49918691.28599.9
2.48-2.6140.41518311.26799.8
2.61-2.7740.29518701.055100
2.77-2.9940.21818630.94999.9
2.99-3.2940.14518630.98999.9
3.29-3.7640.09818851.016100
3.76-4.743.90.05519201.0299.4
4.74-503.90.04520221.149100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.208→41.902 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 1866 10 %
Rwork0.2021 16793 -
obs0.2068 18659 98.85 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.21 Å2 / Biso mean: 30.8683 Å2 / Biso min: 7.53 Å2
Refinement stepCycle: final / Resolution: 2.208→41.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 13 141 3052
Biso mean--50.18 32 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032968
X-RAY DIFFRACTIONf_angle_d0.7034053
X-RAY DIFFRACTIONf_chiral_restr0.028469
X-RAY DIFFRACTIONf_plane_restr0.003542
X-RAY DIFFRACTIONf_dihedral_angle_d11.4781097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2084-2.26810.32241260.26521168129493
2.2681-2.33480.33971400.261238137899
2.3348-2.41020.30551390.24741317145699
2.4102-2.49630.27641430.23621275141899
2.4963-2.59630.26891390.24041268140799
2.5963-2.71440.36271440.23611289143399
2.7144-2.85750.3311500.24291254140499
2.8575-3.03650.27781430.226813301473100
3.0365-3.27080.23751460.211812681414100
3.2708-3.59980.25131430.191313201463100
3.5998-4.12030.21551410.167513331474100
4.1203-5.18970.18031510.14791324147599
5.1897-41.90960.19661610.18214091570100

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