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- PDB-2f09: Solution Structure of the gene product of E. coli gene ydhA -

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Entry
Database: PDB / ID: 2f09
TitleSolution Structure of the gene product of E. coli gene ydhA
ComponentsHypothetical protein ydhA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 8 strand beta-barrel / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


lysozyme inhibitor activity / cell outer membrane
Similarity search - Function
C-type lysozyme inhibitor / Membrane-bound lysozyme-inhibitor of c-type lysozyme / C-type lysozyme inhibitor superfamily / C-type lysozyme inhibitor / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Membrane-bound lysozyme inhibitor of C-type lysozyme
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics
AuthorsShaw, G.S. / Revington, M.J. / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: The solution structure of the Escherichia coli gene product ydhA.
Authors: Shaw, G.S. / Revington, M.J.
History
DepositionNov 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: 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_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Assembly

Deposited unit
A: Hypothetical protein ydhA


Theoretical massNumber of molelcules
Total (without water)11,7361
Polymers11,7361
Non-polymers00
Water00
1


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

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Components

#1: Protein Hypothetical protein ydhA


Mass: 11736.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ydhA / Plasmid: pEt15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P28224
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 0.5 mM ydha U-15N,U-13C, 10mM sodium phosphate, 400 mM NaCl, 10 mM dithiothreitol, 0.01% sodium azide, 1mM benzamidine, pH6.5, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 410 mM / pH: 6.5 / Pressure: ambient / Temperature: 298.0 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian Inc.collection
NMRPipe2.3Frank Delaglio Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, and Ad Baxprocessing
NMRView5.2.2B.A. Johnsondata analysis
CYANA2.032.3Guntert, P., Mumenthaler, C. and Wuthrich, K.refinement
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros,R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges,N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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