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- PDB-2kfu: PknB-phosphorylated Rv1827 -

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Basic information

Entry
Database: PDB / ID: 2kfu
TitlePknB-phosphorylated Rv1827
ComponentsRv1827 pThr 22
KeywordsPROTEIN BINDING / FHA domain / Mycobacterium tuberculosis / phosphorylation / intramolecular interaction / glutamate metabolism / Phosphoprotein
Function / homology
Function and homology information


cell wall / regulation of cellular respiration / negative regulation of glycolytic process / molecular function inhibitor activity / peptidoglycan-based cell wall / protein autophosphorylation / mRNA binding / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glycogen accumulation regulator GarA / Glycogen accumulation regulator GarA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 3
AuthorsSmerdon, S.J. / Nott, T.J. / Kelly, G.
CitationJournal: Sci.Signal. / Year: 2009
Title: An intramolecular switch regulates phosphoindependent FHA domain interactions in Mycobacterium tuberculosis.
Authors: Nott, T.J. / Kelly, G. / Stach, L. / Li, J. / Westcott, S. / Patel, D. / Hunt, D.M. / Howell, S. / Buxton, R.S. / O'Hare, H.M. / Smerdon, S.J.
History
DepositionFeb 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _pdbx_database_status.status_code_cs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rv1827 pThr 22


Theoretical massNumber of molelcules
Total (without water)17,3141
Polymers17,3141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Rv1827 pThr 22


Mass: 17313.738 Da / Num. of mol.: 1 / Mutation: M1V for cloning reasons
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1827, MT1875, MTCY1A11.16c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P64897, UniProt: P9WJA9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HN(CO)CA
1513D HNCO
1613D HNCA
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
21023D 1H-13C NOESY
11113D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium acetate, 50 mM sodium chloride, 0.3-1.0 mM [U-99% 13C; U-99% 15N] Rv1827 pThr 22, 90% H2O/10% D2O90% H2O/10% D2O
220 mM sodium acetate, 50 mM sodium chloride, 0.3-1.0 mM [U-99% 13C; U-99% 15N] Rv1827 pThr 22, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMsodium acetate1
50 mMsodium chloride1
mMRv1827 pThr 22[U-99% 13C; U-99% 15N]0.3-1.01
20 mMsodium acetate2
50 mMsodium chloride2
mMRv1827 pThr 22[U-99% 13C; U-99% 15N]0.3-1.02
Sample conditionspH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
ARIA_1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA_1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1998 / NOE intraresidue total count: 659 / NOE long range total count: 775 / NOE medium range total count: 179 / NOE sequential total count: 385 / Hydrogen bond constraints total count: 82 / Protein phi angle constraints total count: 48 / Protein psi angle constraints total count: 48
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 19

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