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- PDB-1z2t: NMR structure study of anchor peptide Ser65-Leu87 of enzyme achol... -

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Basic information

Entry
Database: PDB / ID: 1z2t
TitleNMR structure study of anchor peptide Ser65-Leu87 of enzyme acholeplasma laidlawii Monoglycosyldiacyl Glycerol Synthase (alMGS) in DHPC micelles
ComponentsAnchor peptide Ser65-Leu87 of alMGS
KeywordsLIPID BINDING PROTEIN / Anchor peptide
Function / homology
Function and homology information


1,2-diacylglycerol 3-alpha-glucosyltransferase / membrane lipid biosynthetic process / glycerol metabolic process / hexosyltransferase activity / magnesium ion binding / plasma membrane
Similarity search - Function
Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
: / Alpha-monoglucosyldiacylglycerol synthase
Similarity search - Component
MethodSOLUTION NMR / distance geometry
AuthorsLind, J. / Barany-Wallje, E. / Ramo, T. / Wieslander, A. / Maler, L.
CitationJournal: To be Published
Title: Structure, position of and membrane-interaction of a putative membrane-anchoring domain of alMGS
Authors: Lind, J. / Barany-Wallje, E. / Ramo, T. / Wieslander, A. / Maler, L.
History
DepositionMar 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 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: Anchor peptide Ser65-Leu87 of alMGS


Theoretical massNumber of molelcules
Total (without water)2,8891
Polymers2,8891
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)24 / 50structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Anchor peptide Ser65-Leu87 of alMGS


Mass: 2888.718 Da / Num. of mol.: 1 / Fragment: Anchor peptide Ser65-Leu87 of alMGS / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: GenBank: 14043013, UniProt: Q93P60*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: Mixing times: 2D-NOESY: 100 ms 2D-TOCSY: 30 and 80 ms

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Sample preparation

DetailsContents: 1 mM alMGS, 100 mM DHPC, 90% H2O, 10%D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsPressure: ambient / Temperature: 310 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
Felix2000.1Accelrysprocessing
DYANA1.5Guntert, P. Mumenthaler, C. Wuthrich, K.structure solution
DYANA1.5Guntert, P., Mumenthaler, C. Wuthrich, K.refinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: the structures are based on a total of 188 restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 50 / Conformers submitted total number: 24

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