+Open data
-Basic information
Entry | Database: PDB / ID: 1swu | ||||||
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Title | STREPTAVIDIN MUTANT Y43F | ||||||
Components | STREPTAVIDIN | ||||||
Keywords | PROTEIN BINDING / BIOTIN BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Freitag, S. / Le Trong, I. / Klumb, L.A. / Stayton, P.S. / Stenkamp, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Atomic resolution structure of biotin-free Tyr43Phe streptavidin: what is in the binding site? Authors: Freitag, S. / Le Trong, I. / Klumb, L.A. / 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 | 1swu.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1swu.ent.gz | 173.6 KB | Display | PDB format |
PDBx/mmJSON format | 1swu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/1swu ftp://data.pdbj.org/pub/pdb/validation_reports/sw/1swu | HTTPS FTP |
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-Related structure data
Related structure data | 1swaS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1), |
-Components
#1: Protein | Mass: 13265.336 Da / Num. of mol.: 4 / Mutation: Y43F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: PET-210 , NOVAGEN, INC., MADISON,WI / Cell line (production host): T7 EXPRESSION SYSTEM / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 #2: Chemical | ChemComp-MRD / ( | #3: Chemical | ChemComp-MPD / ( #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: 1.93 Å3/Da / Density % sol: 36 % | |||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | |||||||||||||||
Components of the solutions |
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Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1998 |
Radiation | Protocol: MONOCHROMATIC / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→50 Å / Num. obs: 149978 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.14→1.2 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.8 / % possible all: 81 |
Reflection | *PLUS Num. measured all: 627749 |
Reflection shell | *PLUS Lowest resolution: 1.2 Å / % possible obs: 81 % / Rmerge(I) obs: 0.144 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SWA Resolution: 1.14→10 Å / Num. parameters: 38361 / Num. restraintsaints: 48997 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (I>2SIGMA(I)) BY 0.05
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-218 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 41 / Occupancy sum hydrogen: 3331.3 / Occupancy sum non hydrogen: 3980.1 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.125 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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