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- PDB-1xo0: High resolution structure of the holliday junction intermediate i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xo0 | ||||||
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Title | High resolution structure of the holliday junction intermediate in cre-loxp site-specific recombination | ||||||
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![]() | HYDROLASE / LIGASE/DNA / CRE RECOMBINASE / HOLLIDAY JUNCTION / RECOMBINATION / COMPLEX (RECOMBINASE-DNA) / LIGASE-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ghosh, K. / Lau, C.K. / Guo, F. / Segall, A.M. / Van Duyne, G.D. | ||||||
![]() | ![]() Title: Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination. Authors: Ghosh, K. / Lau, C.K. / Guo, F. / Segall, A.M. / Van Duyne, G.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.9 KB | Display | ![]() |
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PDB format | ![]() | 146 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.6 KB | Display | ![]() |
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Full document | ![]() | 501.3 KB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 52 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xnsC ![]() 1crxS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE IS A TETRAMER. |
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Components
#1: DNA chain | Mass: 10774.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PART OF HOLLIDAY JUNCTION | ||
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#2: DNA chain | Mass: 10743.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PART OF HOLLIDAY JUNCTION | ||
#3: Protein | Mass: 36549.832 Da / Num. of mol.: 2 / Mutation: R173K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20mM ACETATE BUFFER PH 5.0 40%MPD 20mM CACL2. , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9188 Å / Relative weight: 1 |
Reflection | Resolution: 2→26 Å / Num. all: 67741 / Num. obs: 58491 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.076 |
Reflection shell | Resolution: 2→2.09 Å / Num. unique all: 3025 / % possible all: 84.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CRX Resolution: 2→26 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: The following bond distances are slightly long: peptide bond between chain B residues THR 202 and B LEU 203. phospho diester bridge between chain C nucleotides T 1 and A 2. phospho diester ...Details: The following bond distances are slightly long: peptide bond between chain B residues THR 202 and B LEU 203. phospho diester bridge between chain C nucleotides T 1 and A 2. phospho diester bridge between chain D nucleotides T 1 and A 2.
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Refinement step | Cycle: LAST / Resolution: 2→26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å |