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- PDB-1jj8: 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: 1jj8 | ||||||
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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 / I4 FORM 2 / 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 | ![]() | 39.1 KB | Display | ![]() |
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PDB format | ![]() | 24.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ijwC ![]() 1jj6C ![]() 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 on special symmetry positions |
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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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.423 Å3/Da / Density % sol: 47.27 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.08 MM DNA, 0.04 MM HIN, 25 MM NA ACETATE (PH 4.6), 25 MM MGCL2, 8 MM NACL, 6.3% V/V PEG400, AND 1.25 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM NA ACETATE (PH 4.6), 100 MM MGCL2, ...Details: 0.08 MM DNA, 0.04 MM HIN, 25 MM NA ACETATE (PH 4.6), 25 MM MGCL2, 8 MM NACL, 6.3% V/V PEG400, AND 1.25 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM NA ACETATE (PH 4.6), 100 MM MGCL2, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%. CONDITIONS FOR NATIVE ARE THE SAME EXCEPT THE CONCENTRATION OF MGCL2 IS 5 TIMES SMALLER., pH 4.60, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 21 ℃ / pH: 4.6 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.543 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→25 Å / Num. obs: 3765 / % possible obs: 96.49 % / Observed criterion σ(I): 1 / Redundancy: 15 % / Biso Wilson estimate: 44 Å2 / Rsym value: 0.081 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.75→2.87 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.267 / % possible all: 91.64 |
Reflection | *PLUS % possible obs: 96.5 % / Redundancy: 15 % / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS % possible obs: 91.6 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SIRAS PHASES Resolution: 2.75→25 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: ANISOTROPIC_FIXED_ISOTROPIC / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Bsol: 18.88 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.87 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.353 |