+Open data
-Basic information
Entry | Database: PDB / ID: 4jo6 | ||||||
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Title | Streptavidin complex with SBP-Tag | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / Homotetramer bound to peptides / Biotechnological targeting / Biotin and peptide binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Barrette-Ng, I.H. / Wu, S.C. / Tjia, W.M. / Wong, S.L. / Ng, K.K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: The structure of the SBP-Tag-streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits Authors: Barrette-Ng, I.H. / Wu, S.C. / Tjia, W.M. / Wong, S.L. / Ng, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jo6.cif.gz | 211.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jo6.ent.gz | 171 KB | Display | PDB format |
PDBx/mmJSON format | 4jo6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/4jo6 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/4jo6 | HTTPS FTP |
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-Related structure data
Related structure data | 1sweS 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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-Components
#1: Protein | Mass: 16504.852 Da / Num. of mol.: 4 / Fragment: UNP residues 25-183 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629 #2: Protein/peptide | Mass: 4313.770 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The synthetic peptide was originally isolated from an in vitro selection and evolution experiment. #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 56% Tacsimate, 12%(w/v) glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 18, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→60 Å / Num. obs: 52299 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.5 / Num. unique all: 14270 / Rsym value: 0.424 / % possible all: 72.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SWE Resolution: 1.75→57.54 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.386 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.361 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→57.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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