+Open data
-Basic information
Entry | Database: PDB / ID: 1nqm | ||||||
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Title | Structure of Savm-W120K, streptavidin mutant | ||||||
Components | Streptavidin | ||||||
Keywords | UNKNOWN FUNCTION / avidin / streptavidin / biotin / monomer-monomer interaction / high affinity systems | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Pazy, Y. / Eisenberg-Domovich, Y. / Laitinen, O.H. / Kulomaa, M.S. / Bayer, E.A. / Wilchek, M. / Livnah, O. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2003 Title: Dimer-Tetramer Transition between Solution and Crystalline States of Streptavidin and Avidin Mutants. Authors: Pazy, Y. / Eisenberg-Domovich, Y. / Laitinen, O.H. / Kulomaa, M.S. / Bayer, E.A. / Wilchek, M. / Livnah, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nqm.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nqm.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nqm_validation.pdf.gz | 402.2 KB | Display | wwPDB validaton report |
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Full document | 1nqm_full_validation.pdf.gz | 410.3 KB | Display | |
Data in XML | 1nqm_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1nqm_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqm ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14195.374 Da / Num. of mol.: 4 / Mutation: W120K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Cell line (production host): JM109 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P22629 #2: Chemical | ChemComp-BTN / #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: 2.17 Å3/Da / Density % sol: 43.28 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.45 Details: 25% PEG 6K, 0.3M sodium acetate, 0.1M cac. buffer, pH 6.45, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging 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: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Num. obs: 51529 / % possible obs: 97.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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