+Open data
-Basic information
Entry | Database: PDB / ID: 3rdm | ||||||
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Title | Crystal structure of R7-2 streptavidin complexed with biotin/PEG | ||||||
Components | Streptavidin | ||||||
Keywords | BIOTIN BINDING PROTEIN / Streptavidin variants / improved desthiobiotin binding / opened loop destabilization | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Malashkevich, V.N. / Magalhaes, M. / Czecster, C.M. / Guan, R. / Levy, M. / Almo, S.C. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Evolved streptavidin mutants reveal key role of loop residue in high-affinity binding. Authors: Magalhaes, M.L. / Czekster, C.M. / Guan, R. / Malashkevich, V.N. / Almo, S.C. / Levy, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rdm.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rdm.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 3rdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/3rdm ftp://data.pdbj.org/pub/pdb/validation_reports/rd/3rdm | HTTPS FTP |
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-Related structure data
Related structure data | 3rdoC 3rdqC 3rdsC 3rduC 3rdxC 3re5C 3re6C 2iziS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15966.381 Da / Num. of mol.: 1 / Fragment: UNP Residues 37-164 / Mutation: T90S, W108V, L110T, F29L, S52G, R53S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pCR2.1-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: P22629 |
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#2: Chemical | ChemComp-1PE / |
#3: Chemical | ChemComp-BTN / |
#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: 2.25 Å3/Da / Density % sol: 45.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 MgCl2, 0.1 Bis-Tris, pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 19742 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.077 / Χ2: 2.201 / Net I/σ(I): 11.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 36.21 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IZI Resolution: 1.6→19.17 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2373 / WRfactor Rwork: 0.2091 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8603 / SU B: 3.221 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0958 / SU Rfree: 0.0955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: 50.81 Å2 / Biso mean: 21.471 Å2 / Biso min: 4.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -13.8528 Å / Origin y: -24.4766 Å / Origin z: -2.4905 Å
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Refinement TLS group |
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