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Yorodumi- PDB-1jkr: Testing the Water-Mediated HIN Recombinase DNA Recognition by Sys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jkr | ||||||
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Title | Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / WATER-MEDIATED RECOGNITION / PROTEIN-DNA COMPLEX / HIN RECOMBINASE / T11C MUTANT / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA strand exchange activity / DNA integration / DNA recombination / DNA binding Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Chiu, T.K. / Sohn, C. / Johnson, R.C. / Dickerson, R.E. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Testing water-mediated DNA recognition by the Hin recombinase. Authors: Chiu, T.K. / Sohn, C. / Dickerson, R.E. / Johnson, R.C. #1: Journal: Thesis / Year: 2001 Title: How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase Authors: Chiu, T.K. #2: Journal: Science / Year: 1994 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jkr.cif.gz | 39.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jkr.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/1jkr ftp://data.pdbj.org/pub/pdb/validation_reports/jk/1jkr | HTTPS FTP |
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-Related structure data
Related structure data | 1ijwSC 1jj6C 1jj8C 1jkoC 1jkpC 1jkqC 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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-Components
#1: DNA chain | Mass: 4309.826 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4247.805 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 53.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: HANGING DROP VAPOR DIFFUSION AT 4C, WITH INITIAL CONCENTRATION IN DROP OF 0.10 MM DNA, 0.06 MM HIN, 10 MM TRIS (PH 8.5), 10 MM CACL2, 23 MM NACL, 2.5% 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 TRIS (PH 8.5), 10 MM CACL2, 23 MM NACL, 2.5% V/V PEG400, AND 1.56 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%., pH 8.50, 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: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Detector: CCD / Date: Aug 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: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→24.8 Å / Num. obs: 7102 / % possible obs: 93.23 % / Observed criterion σ(I): 0 / Redundancy: 17 % / Biso Wilson estimate: 69 Å2 / Rsym value: 0.89 / Net I/σ(I): 15.68 |
Reflection shell | Resolution: 2.28→2.38 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.49 / Rsym value: 0.252 / % possible all: 72.14 |
Reflection | *PLUS Redundancy: 17 % / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 72.1 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IJW Resolution: 2.28→24.8 Å / Isotropic thermal model: ANISOTROPIC_FIXED_ISOTROPIC / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Bsol: 100 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→24.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.38 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: 9.28 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.454 |