+Open data
-Basic information
Entry | Database: PDB / ID: 1swp | ||||||
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Title | CORE-STREPTAVIDIN MUTANT W120F IN COMPLEX WITH BIOTIN AT PH 7.5 | ||||||
Components | CORE-STREPTAVIDIN | ||||||
Keywords | BIOTIN-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Freitag, S. / Le Trong, I. / Chilkoti, A. / Klumb, L.A. / Stayton, P.S. / Stenkamp, R.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Structural studies of binding site tryptophan mutants in the high-affinity streptavidin-biotin complex. Authors: Freitag, S. / Le Trong, I. / Chilkoti, A. / Klumb, L.A. / Stayton, P.S. / Stenkamp, R.E. #1: Journal: Protein Sci. / Year: 1998 Title: Thermodynamic and Structural Consequences of Flexible Loop Deletion by Circular Permutation in the Streptavidin-Biotin System Authors: Chu, V. / Freitag, S. / Le Trong, I. / Stenkamp, R.E. / Stayton, P.S. #2: Journal: Protein Sci. / Year: 1997 Title: Structural Studies of the Streptavidin Binding Loop Authors: Freitag, S. / Le Trong, I. / Klumb, L. / 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 | 1swp.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1swp.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 1swp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/1swp ftp://data.pdbj.org/pub/pdb/validation_reports/sw/1swp | HTTPS FTP |
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-Related structure data
Related structure data | 1swhC 1swjC 1swkC 1swlC 1swnC 1swoC 1swqC 1swrC 1sweS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 13242.301 Da / Num. of mol.: 4 / Mutation: W120F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Description: PET-210, NOVAGEN, INC., MADISON,WI / Plasmid: PET-210 / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 #2: Chemical | #3: Chemical | ChemComp-BTQ / | #4: 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: 2.43 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 13, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. obs: 24596 / % possible obs: 90 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 75 |
Reflection | *PLUS Num. measured all: 62223 |
Reflection shell | *PLUS % possible obs: 75 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SWE Resolution: 2→10 Å / Num. parameters: 14951 / Num. restraintsaints: 27450 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: NON CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE APPLIED FOR THE FOUR SUBUNITS OF THE TETRAMER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 3264 / Occupancy sum non hydrogen: 3737 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 24596 / Rfactor all: 0.202 / Rfactor Rfree: 0.278 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.015 |