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- PDB-2n5z: Mycobacterium tuberculosis: a dynamic view of the resuscitation p... -

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Basic information

Entry
Database: PDB / ID: 2n5z
TitleMycobacterium tuberculosis: a dynamic view of the resuscitation promoting factor RpfC catalytic domain
ComponentsResuscitation-promoting factor RpfC
KeywordsHYDROLASE / resuscitation promoting factor / RpfC
Function / homology
Function and homology information


Hydrolases / quorum sensing / regulation of cell population proliferation / hydrolase activity / negative regulation of gene expression / positive regulation of gene expression / extracellular region
Similarity search - Function
Resuscitation-promoting factor, core lysozyme-like domain / Transglycosylase-like domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Resuscitation-promoting factor RpfC
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model13
AuthorsMaione, V. / Russo, L. / Isernia, C.
CitationJournal: Plos One / Year: 2015
Title: NMR Structure and Dynamics of the Resuscitation Promoting Factor RpfC Catalytic Domain.
Authors: Maione, V. / Ruggiero, A. / Russo, L. / De Simone, A. / Pedone, P.V. / Malgieri, G. / Berisio, R. / Isernia, C.
History
DepositionAug 7, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Resuscitation-promoting factor RpfC


Theoretical massNumber of molelcules
Total (without water)8,1801
Polymers8,1801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Resuscitation-promoting factor RpfC


Mass: 8179.935 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: MTCY180.34, rpfC, Rv1884c / Production host: Escherichia coli (E. coli) / References: UniProt: O07747, Hydrolases

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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 1H-15N TOCSY
1313D 1H-15N NOESY
1422D 1H-13C HSQC aliphatic
1522D 1H-13C HSQC aromatic
1623D CBCA(CO)NH
1723D HN(CA)CB
1823D (H)CCH-TOCSY
1923D 1H-13C NOESY aliphatic
11023D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM [U-100% 15N] sodium phosphate, 150 mM [U-100% 15N] sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
220 mM [U-100% 13C; U-100% 15N] sodium phosphate, 150 mM [U-100% 13C; U-100% 15N] sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate-1[U-100% 15N]1
150 mMsodium chloride-2[U-100% 15N]1
20 mMsodium phosphate-3[U-100% 13C; U-100% 15N]2
150 mMsodium chloride-4[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.15 / pH: 6.9 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
VnmrJVariancollection
VnmrJVarianprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1030 / NOE intraresidue total count: 539 / NOE long range total count: 139 / NOE medium range total count: 132 / NOE sequential total count: 220
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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