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- PDB-1jko: 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: 1jko | ||||||
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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 / A10G MUTANT / 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 | ![]() | 38.4 KB | Display | ![]() |
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PDB format | ![]() | 23.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.8 KB | Display | ![]() |
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Full document | ![]() | 463.7 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ijwSC ![]() 1jj6C ![]() 1jj8C ![]() 1jkpC ![]() 1jkqC ![]() 1jkrC S: Starting model for refinement 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: 4340.835 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4216.795 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: 2.65 Å3/Da / Density % sol: 51.74 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP VAPOR DIFFUSION AT 4C, WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA, 0.06 MM HIN, 10 MM HEPES (PH 7.5), 5 MM CACL2, 13 MM NACL, 2.8% V/V PEG400, AND 1.56 MM NA CACODYLATE. ...Details: HANGING DROP VAPOR DIFFUSION AT 4C, WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA, 0.06 MM HIN, 10 MM HEPES (PH 7.5), 5 MM CACL2, 13 MM NACL, 2.8% V/V PEG400, AND 1.56 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM HEPES (PH 7.5), 50 MM CACL2, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%., pH 7.50, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / 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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 1997 |
Radiation | Protocol: MOLECULAR REPLACEMENT WITH 1IJW HAVING THE PROPER DNA SUBSTITUTIONS AS THE STARTING MODEL. Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→14 Å / Num. obs: 6235 / % possible obs: 81.27 % / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 67 Å2 / Rsym value: 0.068 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.24→2.34 Å / Redundancy: 1.49 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.215 / % possible all: 50.8 |
Reflection | *PLUS % possible obs: 81.3 % / Redundancy: 15 % / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 50.8 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 2.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IJW Resolution: 2.24→14 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: 100 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.24→14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.34 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 Rwork: 0.466 / Rfactor obs: 0.466 |