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Yorodumi- PDB-2kqn: Solution structure of the AL-09 H87Y immunoglobulin light chain v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kqn | ||||||
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Title | Solution structure of the AL-09 H87Y immunoglobulin light chain variable domain | ||||||
Components | Ig kappa chain V-I region AU | ||||||
Keywords | IMMUNE SYSTEM / Amyloidosis / Immunoglobulin kappa light chain / homodimer / Bence-Jones protein / Disulfide bond / Immunoglobulin domain / Immunoglobulin V region | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Volkman, B.F. / Peterson, F.C. / Ramirez-Alvarado, M. / Baden, E.M. | ||||||
Citation | Journal: Structure / Year: 2010 Title: A single mutation promotes amyloidogenicity through a highly promiscuous dimer interface. Authors: Peterson, F.C. / Baden, E.M. / Owen, B.A. / Volkman, B.F. / Ramirez-Alvarado, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kqn.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kqn.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2kqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kqn_validation.pdf.gz | 353.1 KB | Display | wwPDB validaton report |
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Full document | 2kqn_full_validation.pdf.gz | 575.1 KB | Display | |
Data in XML | 2kqn_validation.xml.gz | 72 KB | Display | |
Data in CIF | 2kqn_validation.cif.gz | 110.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/2kqn ftp://data.pdbj.org/pub/pdb/validation_reports/kq/2kqn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 12154.369 Da / Num. of mol.: 2 / Fragment: Immunoglobulin kappa light chain / Mutation: H87Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold(DE3) |
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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 mM [U-100% 13C; U-100% 15N] AL-09 H87Y-1, 10 mM [U-2H] MES-2, 0.02 % sodium azide-3, 95% H2O, 5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 8 / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT Software ordinal: 1 Details: HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 2104 NOE CONSTRAINTS (341 INTRA, 394 SEQUENTIAL, 265 MEDIUM, 1027 INTRAMONOMER LONG RANGE AND 77 INTERMONOMER NOE CONSTRAINTS) AND 149 PHI AND ...Details: HOMODIMER STRUCTURES ARE BASED ON A TOTAL OF 2104 NOE CONSTRAINTS (341 INTRA, 394 SEQUENTIAL, 265 MEDIUM, 1027 INTRAMONOMER LONG RANGE AND 77 INTERMONOMER NOE CONSTRAINTS) AND 149 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS PER MONOMER. CONSTRAINTS WERE ASSIGNED AND VALIDATED IN ONE MONOMER AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINTS IN THE SECOND MONOMER. | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2104 / NOE intraresidue total count: 341 / NOE long range total count: 1104 / NOE medium range total count: 265 / NOE sequential total count: 394 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 75 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |