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- PDB-2m1z: Solution structure of uncharacterized protein lmo0427 -

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Basic information

Entry
Database: PDB / ID: 2m1z
TitleSolution structure of uncharacterized protein lmo0427
ComponentsLmo0427 protein
KeywordsTRANSFERASE / homolog PTS system IIB component / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity / protein-phosphocysteine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / plasma membrane
Similarity search - Function
Phosphotransferase system, fructose-specific IIB subunit / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZhang, Y. / Winsor, J. / Radhakrishnan, I. / Anderson, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Solution structure of hypothetical protein lmo0427
Authors: Zhang, Y. / Winsor, J. / Radhakrishnan, I. / Anderson, W.
History
DepositionDec 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo0427 protein


Theoretical massNumber of molelcules
Total (without water)11,3951
Polymers11,3951
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 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lmo0427 protein


Mass: 11395.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo0427 / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y9U3

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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 CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1523D (H)CCH-TOCSY
1623D (H)CCH-COSY
1713D 1H-15N NOESY
1823D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-95% 13C; U-95% 15N] Listeria monocytogenes EGD-e, 20 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-95% 13C; U-95% 15N] Listeria monocytogenes EGD-e, 20 mM potassium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMListeria monocytogenes EGD-e-1[U-95% 13C; U-95% 15N]1
20 mMpotassium phosphate-21
100 mMsodium chloride-31
1.2 mMListeria monocytogenes EGD-e-4[U-95% 13C; U-95% 15N]2
20 mMpotassium phosphate-52
100 mMsodium chloride-62
Sample conditionsIonic strength: 0.2 / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Zhengrong and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 20

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