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Yorodumi- PDB-1kl3: an engineered streptavidin with improved affinity for the strep-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kl3 | ||||||
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Title | an engineered streptavidin with improved affinity for the strep-tag II peptide : SAm1-StrepII | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / BIOTIN / PROTEIN ENGINEERING / STREP-TAG / STREPTAVIDIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Korndoerfer, I.P. / Skerra, A. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site. Authors: Korndorfer, I.P. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kl3.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kl3.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/1kl3 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/1kl3 | HTTPS FTP |
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-Related structure data
Related structure data | 1kffC 1kl4C 1kl5C 1swuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is one of the tetramers in the asymmetric unit |
-Components
#1: Protein | Mass: 13383.561 Da / Num. of mol.: 4 / Mutation: E44V,S45T,V47R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pSA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 #2: Protein/peptide | Mass: 1174.263 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: The strep-tag II peptide is chemically synthesized and was selected by synthetic peptide spot assays from a subset of strep-tag derivatives. #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 100 mM Na2HPO4, 1.3-M (NH4)2SO4, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 21, 2001 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36 Å / Num. obs: 49002 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rsym value: 0.04 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.38 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4648 / Rsym value: 0.348 / % possible all: 90.3 |
Reflection | *PLUS Lowest resolution: 99 Å / Num. measured all: 126949 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 90.3 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1SWU Resolution: 1.7→36 Å / SU B: 3.021 / SU ML: 0.101 / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.447 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.75 Å
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Refinement | *PLUS Rfactor obs: 0.175 / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.43 / Rfactor Rwork: 0.41 |