+Open data
-Basic information
Entry | Database: PDB / ID: 3t6l | ||||||
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Title | Y54F mutant of core streptavidin | ||||||
Components | Streptavidin | ||||||
Keywords | BIOTIN BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Baugh, L. / Le Trong, I. / Stayton, P.S. / Stenkamp, R.E. / Lybrand, T.P. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Second-Contact Shell Mutation Diminishes Streptavidin-Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics. Authors: Baugh, L. / Le Trong, I. / Cerutti, D.S. / Mehta, N. / Gulich, S. / Stayton, P.S. / Stenkamp, R.E. / Lybrand, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t6l.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t6l.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 3t6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t6l_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 3t6l_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 3t6l_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 3t6l_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t6l ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t6l | HTTPS FTP |
-Related structure data
Related structure data | 3t6fC 1mm9S 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13265.336 Da / Num. of mol.: 1 / Fragment: UNP residues 37-163 / Mutation: Y54F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22629 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 2.5 M sodium chloride, 0.1 M sodium-potassium phosphate (30% ethylene glycol cryoprotectant), pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2011 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→36.628 Å / Num. all: 35684 / Num. obs: 35679 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6957 / % possible all: 93.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MM9 Resolution: 1.3→36.628 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1554 / WRfactor Rwork: 0.1316 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9309 / SU B: 1 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0387 / SU Rfree: 0.0384 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 51.57 Å2 / Biso mean: 17.4686 Å2 / Biso min: 8.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→36.628 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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