+Open data
-Basic information
Entry | Database: PDB / ID: 2m5a | ||||||
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Title | Protein A binding by an engineered Affibody molecule | ||||||
Components |
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Keywords | PROTEIN BINDING / binding protein / protein engineering / protein A / Z domain / Affibody molecule | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) artificial gene (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Hard, T. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2013 Title: High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule. Authors: Lindborg, M. / Dubnovitsky, A. / Olesen, K. / Bjorkman, T. / Abrahmsen, L. / Feldwisch, J. / Hard, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m5a.cif.gz | 764.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m5a.ent.gz | 653.6 KB | Display | PDB format |
PDBx/mmJSON format | 2m5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m5a_validation.pdf.gz | 411.5 KB | Display | wwPDB validaton report |
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Full document | 2m5a_full_validation.pdf.gz | 634 KB | Display | |
Data in XML | 2m5a_validation.xml.gz | 35 KB | Display | |
Data in CIF | 2m5a_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/2m5a ftp://data.pdbj.org/pub/pdb/validation_reports/m5/2m5a | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 6648.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Description: In-house standard expression vector with T7 promoter Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P38507 |
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#2: Protein | Mass: 6394.071 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) Description: In-house standard expression vector with T7 promoter Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.095 / pH: 5.6 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 50 / Conformers submitted total number: 20 |