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- PDB-2rqm: NMR Solution Structure of Mesoderm Development (MESD) - open conf... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2rqm
TitleNMR Solution Structure of Mesoderm Development (MESD) - open conformation
ComponentsMesoderm development candidate 2
KeywordsCHAPERONE
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #640 / LRP chaperone MESD / Chaperone for wingless signalling and trafficking of LDL receptor / ACT domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsD45-K184 Conserved Core Region
AuthorsKoehler, C. / Lighthouse, J.K. / Werther, T. / Andersen, O.M. / Diehl, A. / Schmieder, P. / Holdener, B.C. / Oschkinat, H.
CitationJournal: Structure / Year: 2011
Title: The Structure of MESD45-184 Brings Light into the Mechanism of LDLR Family Folding
Authors: Kohler, C. / Lighthouse, J.K. / Werther, T. / Andersen, O.M. / Diehl, A. / Schmieder, P. / Du, J. / Holdener, B.C. / Oschkinat, H.
History
DepositionAug 14, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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)16,1481
Polymers16,1481
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mesoderm development candidate 2


Mass: 16148.112 Da / Num. of mol.: 1
Fragment: D45-K184 conserved core region, UNP residues 45-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mesdc2 / Plasmid: pET-30 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ERE7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: D45-K184 Conserved Core Region
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1242D 1H-15N HSQC
1312D 1H-13C HSQC
1423D CBCA(CO)NH
1523D CBCANNH
1623D HNCO
1723D HN(CA)CO
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11023D H(CCCO)NH-TOCSY
11123D (H)CC(CO)NH-TOCSY
11233D 1H-15N NOESY
11313D 1H-13C NOESY
11432D 1H-15N HSQC coupled
11532D 1H-15N HSQC 15N T1-edited
11632D 1H-15N HSQC 15N T2-edited

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-100% 13C; U-100% 15N] MESD, 20mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 0.1mM EDTA, 100% D2O100% D2O
21mM [U-100% 13C; U-100% 15N] MESD, 20mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 0.1mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31mM [U-100% 15N] MESD, 20mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 0.1mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
41mM [U-100% 15N] MESD, 20mM sodium phosphate, 50mM sodium chloride, 0.02% sodium azide, 0.1mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMESD[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
0.02 %sodium azide1
0.1 mMEDTA1
1 mMMESD[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
0.02 %sodium azide2
0.1 mMEDTA2
1 mMMESD[U-100% 15N]3
20 mMsodium phosphate3
50 mMsodium chloride3
0.02 %sodium azide3
0.1 mMEDTA3
1 mMMESD[U-100% 15N]4
20 mMsodium phosphate4
50 mMsodium chloride4
0.02 %sodium azide4
0.1 mMEDTA4
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVBrukerAV9001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddardpeak picking
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
CYANA2Guntert, Mumenthaler, Wuthrichstructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra, Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 527 / NOE intraresidue total count: 0 / NOE long range total count: 147 / NOE medium range total count: 107 / NOE sequential total count: 273 / Hydrogen bond constraints total count: 106 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 113 / Protein psi angle constraints total count: 113
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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