+Open data
-Basic information
Entry | Database: PDB / ID: 2kgl | ||||||
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Title | NMR solution structure of MESD | ||||||
Components | Mesoderm development candidate 2 | ||||||
Keywords | CHAPERONE / MESD / LRP5/6 / YWTD / Wnt | ||||||
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 | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Chen, J. / Wang, J. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Two Structural and Functional Domains of MESD Required for Proper Folding and Trafficking of LRP5/6. Authors: Chen, J. / Liu, C.C. / Li, Q. / Nowak, C. / Bu, G. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kgl.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kgl.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2kgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kgl_validation.pdf.gz | 344.2 KB | Display | wwPDB validaton report |
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Full document | 2kgl_full_validation.pdf.gz | 510.1 KB | Display | |
Data in XML | 2kgl_validation.xml.gz | 74.5 KB | Display | |
Data in CIF | 2kgl_validation.cif.gz | 90 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/2kgl ftp://data.pdbj.org/pub/pdb/validation_reports/kg/2kgl | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 22074.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mesdc2 / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ERE7 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8-1.0 mM MESD, 25 mM sodium chloride, 10 mM EDTA, 10 mM DTT, 0.1 mM sodium azide, 25 mM sodium phosphate, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | pH: 6.8 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR constraints | NOE constraints total: 1646 / NOE intraresidue total count: 171 / NOE long range total count: 397 / NOE medium range total count: 568 / NOE sequential total count: 510 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 132 / Protein psi angle constraints total count: 132 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Average torsion angle constraint violation: 2.53 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 6.61 ° / Maximum upper distance constraint violation: 0.28 Å / Torsion angle constraint violation method: TALOS | ||||||||||||
NMR ensemble rms | Distance rms dev: 0.0062 Å / Distance rms dev error: 0.0013 Å |