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- PDB-5e0y: Crystal Structure of PASTA Domain 4 of Mycobacterium tuberculosis... -

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Basic information

Entry
Database: PDB / ID: 5e0y
TitleCrystal Structure of PASTA Domain 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 / response to host immune response / acetyltransferase activator activity / negative regulation of fatty acid biosynthetic process / negative regulation of catalytic activity / positive regulation of catalytic activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / positive regulation of DNA binding / negative regulation of protein binding ...negative regulation of growth rate / response to host immune response / acetyltransferase activator activity / negative regulation of fatty acid biosynthetic process / negative regulation of catalytic activity / positive regulation of catalytic activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / positive regulation of DNA binding / negative regulation of protein binding / manganese ion binding / regulation of cell shape / non-specific serine/threonine protein kinase / peptidyl-serine phosphorylation / protein kinase activity / protein autophosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein phosphorylation / membrane => GO:0016020 / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Trypsin Inhibitor V; Chain A - #20 / PASTA domain profile. / PASTA domain / PASTA domain / PASTA / Trypsin Inhibitor V; Chain A / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Trypsin Inhibitor V; Chain A - #20 / PASTA domain profile. / PASTA domain / PASTA domain / PASTA / Trypsin Inhibitor V; Chain A / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / 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 (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PknB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3169
Polymers7,7931
Non-polymers5238
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-147 kcal/mol
Surface area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.658, 41.658, 122.517
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-701-

ZN

21A-702-

ZN

31A-832-

HOH

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Components

#1: Protein Serine/threonine-protein kinase PknB


Mass: 7792.748 Da / Num. of mol.: 1 / Fragment: UNP residues 558-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (unknown) / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn
#3: 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M zinc acetate, 0.1 M imidazole pH 8, and 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.2824 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 4409 / % possible obs: 92.4 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.097 / Χ2: 1.123 / Net I/av σ(I): 21.11 / Net I/σ(I): 21.4 / Num. measured all: 67586
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.033.60.362980.9644.3
2.03-2.074.10.2871421.11963.7
2.07-2.114.40.2771681.37271.5
2.11-2.155.60.251771.13179.7
2.15-2.26.60.2032121.29389.5
2.2-2.257.30.2122051.22192.8
2.25-2.3190.1742341.18798.3
2.31-2.37100.2052141.158100
2.37-2.44130.2082411.257100
2.44-2.5216.20.172231.142100
2.52-2.6120.70.1452481.105100
2.61-2.7122.20.1412151.108100
2.71-2.8421.70.1252431.107100
2.84-2.9921.30.1112491.273100
2.99-3.1721.90.0922301.072100
3.17-3.4221.20.0852421.156100
3.42-3.7620.80.0812471.045100
3.76-4.3120.20.0742511.037100
4.31-5.4319.50.0892601.059100
5.43-5016.50.083101.03899.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
HKL-2000data scaling
SOLVEphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.001→34.608 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2639 436 10.04 %
Rwork0.2153 3906 -
obs0.2201 4342 92.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.15 Å2 / Biso mean: 24.1152 Å2 / Biso min: 3.86 Å2
Refinement stepCycle: final / Resolution: 2.001→34.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms521 0 9 50 580
Biso mean--37.14 31.8 -
Num. residues----68
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005565
X-RAY DIFFRACTIONf_angle_d0.908772
X-RAY DIFFRACTIONf_chiral_restr0.03478
X-RAY DIFFRACTIONf_plane_restr0.005107
X-RAY DIFFRACTIONf_dihedral_angle_d15.037206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0012-2.29070.30131140.23591012112675
2.2907-2.88580.28221540.230513841538100
2.8858-34.61280.24631680.203415101678100

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