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- PDB-1wfr: Solution structure of the conserved hypothetical protein TT1886, ... -

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Basic information

Entry
Database: PDB / ID: 1wfr
TitleSolution structure of the conserved hypothetical protein TT1886, possibly sterol carrier protein, from Thermus Thermophilus HB8
ComponentsHypothetical Protein TT1886
KeywordsLIPID BINDING PROTEIN / STEROL CARRIER PROTEIN / STRUCTURAL GENOMICS / LIPID BINDING / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologySCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta / SCP2 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGoroncy, A. / Kigawa, T. / Koshiba, S. / Tomizawa, T. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the conserved hypothetical protein TT1886, possibly sterol carrier protein, from Thermus Thermophilus HB8
Authors: Goroncy, A. / Kigawa, T. / Koshiba, S. / Tomizawa, T. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S.
History
DepositionMay 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical Protein TT1886


Theoretical massNumber of molelcules
Total (without water)15,0781
Polymers15,0781
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 target function

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Components

#1: Protein Hypothetical Protein TT1886


Mass: 15078.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Description: Cell-free protein synthesis / Plasmid: P030826-87 / References: UniProt: Q5SL92

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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

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Sample preparation

DetailsContents: 1.09mM TT1886 U-15N, 13C; 20mM phosphate buffer Na; 100mM NaCl, 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 318 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR2.6BRUKERcollection
NMRPipe20031121FRANK DELAGLIOprocessing
NMRVIEW5.0.14BRUCE A. JOHNSONdata analysis
KUJIRA0.899NAOHIRO KOBAYASHIdata analysis
CYANA2.0.26GUENTERT, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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