[English] 日本語
Yorodumi- PDB-1ie5: NMR STRUCTURE OF THE THIRD IMMUNOGLOBULIN DOMAIN FROM THE NEURAL ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ie5 | ||||||
---|---|---|---|---|---|---|---|
Title | NMR STRUCTURE OF THE THIRD IMMUNOGLOBULIN DOMAIN FROM THE NEURAL CELL ADHESION MOLECULE. | ||||||
Components | NEURAL CELL ADHESION MOLECULE | ||||||
Keywords | CELL ADHESION / Intermediate Immunoglobulin fold | ||||||
Function / homology | Function and homology information synaptic membrane adhesion / homophilic cell adhesion via plasma membrane adhesion molecules / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | SOLUTION NMR / simulated annealing restrained molecular dynamics | ||||||
Authors | Atkins, A.R. / Chung, J. / Deechongkit, S. / Little, E.B. / Edelman, G.M. / Wright, P.E. / Cunningham, B.A. / Dyson, H.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Solution structure of the third immunoglobulin domain of the neural cell adhesion molecule N-CAM: can solution studies define the mechanism of homophilic binding? Authors: Atkins, A.R. / Chung, J. / Deechongkit, S. / Little, E.B. / Edelman, G.M. / Wright, P.E. / Cunningham, B.A. / Dyson, H.J. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE PROTEIN IS A FRAGMENT CONSISTING OF THE THIRD IMMUNOGLOBULIN DOMAIN. The residue ...SEQUENCE THE PROTEIN IS A FRAGMENT CONSISTING OF THE THIRD IMMUNOGLOBULIN DOMAIN. The residue numbers that are referred to (183-288) are for the processed protein, after removal of the signal sequence. The signal sequence is included in the SwissProt database, hence the discrepancy in the numbering. The correct match with the database numbering is with residues 202 -307, with an additional N-terminal glycine introducing in the cloning. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ie5.cif.gz | 633.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ie5.ent.gz | 556.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ie5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ie5_validation.pdf.gz | 354.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ie5_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 1ie5_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 1ie5_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/1ie5 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/1ie5 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 11851.091 Da / Num. of mol.: 1 / Fragment: THIRD IMMUNOGLOBULIN DOMAIN, RESIDUES 183-288 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Organ: BRAIN / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13590 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||
NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
-Sample preparation
Details | Contents: 1mM IgIII U-15N,13C; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: no salt / pH: 6.8 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing restrained molecular dynamics / Software ordinal: 1 Details: The structure is based on 1461 unique NOE-derived restraints, 393 ambiguous NOE-derived restraints, and 131 dihedral angle restraints. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |