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- PDB-2gpf: Solution NMR Structure of Protein PA22412 from Pseudomonas aerugi... -

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Basic information

Entry
Database: PDB / ID: 2gpf
TitleSolution NMR Structure of Protein PA22412 from Pseudomonas aeruginosa. Northeast Structural Genomics Consortium Target PaT86, Ontario Centre for Structural Proteomics Target PA2412.
Componentsconserved hypothetical protein PA2412
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / BETA/ALPHA protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


pyoverdine biosynthetic process / siderophore biosynthetic process / cytosol
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / MbtH-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsLemak, A. / Lukin, J.A. / Yee, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of PA2412 protein determined using ABACUS protocol
Authors: Lemak, A. / Lukin, J.A. / Yee, A. / Arrowsmith, C.H.
History
DepositionApr 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein PA2412


Theoretical massNumber of molelcules
Total (without water)8,4551
Polymers8,4551
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein conserved hypothetical protein PA2412


Mass: 8454.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2412 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3(gold) / References: GenBank: 9948456, UniProt: Q9I169*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131J MODULATED HSQC for RDC

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Sample preparation

DetailsContents: 0.6mM pa2412, U-15N,13C, 450 mM NaCl, 10 mM MOPS, 1 mM Benzamidine, 10 mM DTT, 10 mM ZnSO4, 0.01% NAN3, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 450 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, F.processing
Sparky3.1Goddard, T.D.data analysis
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: 1483 NOE-derived distances constraints, 78 dihedral angle restraints, 40 RDC restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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