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- PDB-2i9s: The solution structure of the core of mesoderm development (MESD). -

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Basic information

Entry
Database: PDB / ID: 2i9s
TitleThe solution structure of the core of mesoderm development (MESD).
ComponentsMesoderm development candidate 2
KeywordsCHAPERONE / ferredoxin-like-fold
Function / homology
Function and homology information


positive regulation of skeletal muscle acetylcholine-gated channel clustering / protein localization to cell surface / low-density lipoprotein particle receptor binding / mesoderm development / phagocytosis / ossification / Wnt signaling pathway / protein folding / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
LRP chaperone MESD / Chaperone for wingless signalling and trafficking of LDL receptor / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsKoehler, C. / Andersen, O. / Diehl, A. / Schmieder, P. / Krause, G. / Oschkinat, H.
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2006
Title: The solution structure of the core of mesoderm development (MESD), a chaperone for members of the LDLR-family
Authors: Kohler, C. / Andersen, O.M. / Diehl, A. / Krause, G. / Schmieder, P. / Oschkinat, H.
History
DepositionSep 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mesoderm development candidate 2


Theoretical massNumber of molelcules
Total (without water)10,9571
Polymers10,9571
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 Mesoderm development candidate 2 / MESD


Mass: 10956.518 Da / Num. of mol.: 1 / Fragment: P89-K184 core region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mesdc2 / Plasmid: pET-30 Xa/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9ERE7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM MESD_89_184 U-15N,13C, 20mM phosphate buffer pH 5,5, 50mM NaCl, 0,1mM EDTA, 0,2% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
21mM MESD_89_184 U-15N, 20mM phosphate buffer pH 5,5, 50mM NaCl, 0,1mM EDTA, 0,2% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 5.5 / 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 DRXBrukerDRX6001
Bruker AVBrukerAV9002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
TopSpin1.5Bruker Biospincollection
Sparky3.106Goddarddata analysis
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR2.15Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure is based on 822 interresidual distance restraints, 146 dihedral angle restraints (TALOS) and 84 hydrogen bond 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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