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Yorodumi- PDB-1mm9: Streptavidin Mutant with Insertion of Fibronectin Hexapeptide, in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mm9 | ||||||
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Title | Streptavidin Mutant with Insertion of Fibronectin Hexapeptide, 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: 1.66 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 | 1mm9.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mm9.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mm9_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 1mm9_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 1mm9_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 1mm9_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mm9 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mm9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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: 13564.644 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: 2.27 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: Jan 29, 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: 1.66→50 Å / Num. all: 17197 / Num. obs: 17197 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.66→1.68 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.2 / Num. unique all: 689 / % possible all: 81.4 |
Reflection | *PLUS Highest resolution: 1.65 Å / % possible obs: 98.9 % / Num. measured all: 240518 |
Reflection shell | *PLUS Highest resolution: 1.65 Å / % possible obs: 81.4 % |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous / Resolution: 1.66→20 Å / Num. parameters: 9480 / Num. restraintsaints: 12020 / 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: 3 / Occupancy sum hydrogen: 877 / Occupancy sum non hydrogen: 1038.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.65 Å / Lowest resolution: 20 Å / Rfactor obs: 0.145 / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.134 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.176 / Rfactor Rwork: 0.119 / Rfactor obs: 0.13 |