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- PDB-1kdl: Solution structure of the amphipathic domain of YopD from Yersinia -

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Basic information

Entry
Database: PDB / ID: 1kdl
TitleSolution structure of the amphipathic domain of YopD from Yersinia
ComponentsYOPD protein
KeywordsSTRUCTURAL PROTEIN / YERSINIA / YOPD / AMPHIPATHIC ALPHA HELIX / BETA TURN
Function / homologyYopD-like / YopD protein / host cell membrane / extracellular region / membrane / Type 3 secretion system translocon protein SctB
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsTengel, T. / Sethson, I. / Francis, M.S.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Conformational analysis by CD and NMR spectroscopy of a peptide encompassing the amphipathic domain of YopD from Yersinia.
Authors: Tengel, T. / Sethson, I. / Francis, M.S.
History
DepositionNov 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list ...pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YOPD protein


Theoretical massNumber of molelcules
Total (without water)2,7681
Polymers2,7681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 150structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein/peptide YOPD protein


Mass: 2768.195 Da / Num. of mol.: 1 / Fragment: 278-300 / Source method: obtained synthetically
Details: The peptide was chemically synthesized and is found in the cytosol and membrane locations. The sequence of the peptide is naturally found in YERSINIA PESTIS (bacteria).
References: UniProt: Q06131

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
14115N HSQC
15113C HSQC

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Sample preparation

DetailsContents: 3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE
Solvent system: 50% H2O; 10 D2O; 40% TFE
Sample conditionsIonic strength: 20 mM SODIUM PHOSPHATE BUFFER / pH: 4.5 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 DRXBrukerDRX6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerrefinement
XwinNMR2.6Brukerdata analysis
MARDIGRAS3Borgiasiterative matrix relaxation
TALOS98.040.21.02Cornilescudata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STANDARD SIMULATED ANNEALING PROTOCOL USING XPLOR 3.851. DIHEDRAL RESTRAINTS WERE OBTAINED WITH TALOS
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 1

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