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- PDB-2myi: Solution Structure of Crc from P. syringae Lz4W -

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Basic information

Entry
Database: PDB / ID: 2myi
TitleSolution Structure of Crc from P. syringae Lz4W
ComponentsExodeoxyribonuclease III
KeywordsRNA BINDING PROTEIN / Crc / Catabolite Repression Control Protein
Function / homology:
Function and homology information
Biological speciesPseudomonas sp. Lz4W (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDeshmukh, M.V. / Sharma, R.
CitationJournal: J.Magn.Reson. / Year: 2022
Title: Crc of Pseudomonas syringae Lz4W utilizes the dominant RNA binding site for mutually exclusive interactions with Hfq:mRNA and CrcY/Z RNA
Authors: Sharma, R. / Paul, J. / Paturi, S. / Ray, M.K. / Deshmukh, M.V.
History
DepositionJan 25, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exodeoxyribonuclease III


Theoretical massNumber of molelcules
Total (without water)29,9301
Polymers29,9301
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Exodeoxyribonuclease III /


Mass: 29929.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. Lz4W (bacteria) / Gene: B195_00495 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M5QNE2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 400 uM [U-100% 15N] Crc, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 400 uM / Component: Crc-1 / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 0.215 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1036 / NOE intraresidue total count: 74 / NOE long range total count: 522 / NOE medium range total count: 514 / NOE sequential total count: 368 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0
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: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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