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- PDB-1jj6: Testing the Water-Mediated Hin Recombinase DNA Recognition by Sys... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jj6 | ||||||
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Title | Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations. | ||||||
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![]() | DNA BINDING PROTEIN/DNA / WATER-MEDIATED RECOGNITION / PROTEIN-DNA COMPLEX / HIN RECOMBINASE / I5 / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | ![]() DNA strand exchange activity / DNA integration / DNA recombination / DNA binding Similarity search - Function | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chiu, T.K. / Sohn, C. / Johnson, R.C. / Dickerson, R.E. | ||||||
![]() | ![]() Title: Testing water-mediated DNA recognition by the Hin recombinase. Authors: Chiu, T.K. / Sohn, C. / Dickerson, R.E. / Johnson, R.C. #1: ![]() Title: How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase Authors: Chiu, T.K. #2: ![]() Title: Hin Recombinase Bound to DNA: The Origin of Specificity in Major and Minor Groove Interactions Authors: Feng, J.A. / Johnson, R.C. / Dickerson, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.6 KB | Display | ![]() |
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PDB format | ![]() | 24.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 460.6 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ijwC ![]() 1jj8C ![]() 1jkoC ![]() 1jkpC ![]() 1jkqC ![]() 1jkrC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 4436.707 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4231.806 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 6047.051 Da / Num. of mol.: 1 / Fragment: RESIDUES 139 TO 190 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / References: UniProt: P03013 |
#4: Chemical | ChemComp-TRS / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 52.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Hanging drop vapor diffusion at 4C, with initial concentration in drop of 0.13 mM DNA, 0.33 mM Hin, 46 mM Tris (pH 8.5), 46 mM CaCl2, 63 mM NaCl, 11.6% v/v PEG400, and 2.03 mM Na cacodylate. ...Details: Hanging drop vapor diffusion at 4C, with initial concentration in drop of 0.13 mM DNA, 0.33 mM Hin, 46 mM Tris (pH 8.5), 46 mM CaCl2, 63 mM NaCl, 11.6% v/v PEG400, and 2.03 mM Na cacodylate. Reservoir solution contains 100 mM Tris (pH 8.5), 100 mM CaCl2, 100 mM NaCl, and 25% PEG400. Concentration of PEG400 in reservoir solution was increased in 5% increments to 35%., VAPOR DIFFUSION, HANGING DROP, temperature 280K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K Details: MULTIPLE WAVELENGTH WITH ANOMALOUS SCATTERING USING THREE IODINE AND ONE BROMINE DERIVATIVES. THE IODINE DERIVATIVES REPLACE THYMINE AT POSITIONS 4, 5, AND 7+19 WITH 5-IODO URACIL. THE ...Details: MULTIPLE WAVELENGTH WITH ANOMALOUS SCATTERING USING THREE IODINE AND ONE BROMINE DERIVATIVES. THE IODINE DERIVATIVES REPLACE THYMINE AT POSITIONS 4, 5, AND 7+19 WITH 5-IODO URACIL. THE BROMINE DERIVATIVE REPLACES CYTOSINE AT POSITION 18 WITH 5-BROMO CYTOSINE. |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jun 1, 1999 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 6695 / % possible obs: 89.55 % / Observed criterion σ(I): 0 / Redundancy: 43 % / Biso Wilson estimate: 54 Å2 / Rsym value: 0.067 / Net I/σ(I): 21.07 |
Reflection shell | Resolution: 2.3→2.4 Å / Mean I/σ(I) obs: 6.34 / Rsym value: 0.192 / % possible all: 55.33 |
Reflection | *PLUS Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 55.3 % / Rmerge(I) obs: 0.19 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: MIRAS PHASES Resolution: 2.3→30 Å / Isotropic thermal model: ANISOTROPIC_FIXED_ISOTROPIC / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Bsol: 100 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.38 / % reflection Rfree: 6.7 % / Rfactor Rwork: 0.356 / Rfactor obs: 0.356 |