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Yorodumi- PDB-1moy: Streptavidin Mutant with Osteopontin Hexapeptide Insertion Includ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1moy | ||||||
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Title | Streptavidin Mutant with Osteopontin Hexapeptide Insertion Including RGD | ||||||
Components | Streptavidin | ||||||
Keywords | Biotin-binding protein / tetramer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / isomorphous / Resolution: 1.55 Å | ||||||
Authors | Le Trong, I. / McDevitt, T.C. / Nelson, K.E. / Stayton, P.S. / Stenkamp, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structural characterization and comparison of RGD cell-adhesion recognition sites engineered into streptavidin. Authors: Le Trong, I. / McDevitt, T.C. / Nelson, K.E. / Stayton, P.S. / Stenkamp, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1moy.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1moy.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 1moy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/1moy ftp://data.pdbj.org/pub/pdb/validation_reports/mo/1moy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13566.660 Da / Num. of mol.: 1 / 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 | ||
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#2: Chemical | #3: 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: 2.24 Å3/Da / Density % sol: 51.71 % | |||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: MPD, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
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: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 20844 / Num. obs: 20844 / % possible obs: 99.9 % / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 1.55→1.58 Å / Rmerge(I) obs: 0.593 / % possible all: 99.4 |
Reflection | *PLUS Num. obs: 20871 / Num. measured all: 486781 |
Reflection shell | *PLUS % possible obs: 99.4 % / Mean I/σ(I) obs: 4.2 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous / Resolution: 1.55→10 Å / Num. parameters: 9537 / Num. restraintsaints: 12733 / 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: 7 / Occupancy sum hydrogen: 901 / Occupancy sum non hydrogen: 1015.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→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 / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.13 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.175 / Rfactor Rwork: 0.122 / Rfactor obs: 0.123 |