+Open data
-Basic information
Entry | Database: PDB / ID: 1mk5 | ||||||
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Title | Wildtype Core-Streptavidin with Biotin at 1.4A. | ||||||
Components | Streptavidin | ||||||
Keywords | Biotin-binding protein / homodimer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS / Resolution: 1.4 Å | ||||||
Authors | Hyre, D.E. / Le Trong, I. / Merritt, E.A. / Green, N.M. / Stenkamp, R.E. / Stayton, P.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Cooperative hydrogen bond interactions in the streptavidin-biotin system Authors: Hyre, D.E. / Le Trong, I. / Merritt, E.A. / Eccleston, J.F. / Green, N.M. / Stenkamp, R.E. / Stayton, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mk5.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mk5.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mk5 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mk5 | HTTPS FTP |
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-Related structure data
Related structure data | 1mepC 1df8S 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: 13281.336 Da / Num. of mol.: 2 / Fragment: Core Streptavidin (residues 13-139) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Gene: core streptavidin / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22629 #2: Chemical | #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: 1.86 Å3/Da / Density % sol: 33.8 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: ammonium sulphate, sodium acetate, sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 44171 / Num. obs: 44171 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.5 / % possible all: 93.4 |
Reflection | *PLUS Num. measured all: 383001 |
Reflection shell | *PLUS % possible obs: 93.4 % / Rmerge(I) obs: 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS Starting model: 1DF8 Resolution: 1.4→10 Å / Num. parameters: 18964 / Num. restraintsaints: 23730 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 1690 / Occupancy sum non hydrogen: 2069 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 38979 / Rfactor Rwork: 0.128 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |