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- PDB-1bp7: GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bp7 | ||||||
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Title | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | ||||||
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![]() | TRANSCRIPTION/DNA / ENDONUCLEASE / GROUP I MOBILE INTRON / INTRON HOMING / CHLOROPLAST DNA / LAGLIDADG MOTIF / DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jurica, M.S. / Monnat Junior, R.J. / Stoddard, B.L. | ||||||
![]() | ![]() Title: DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI. Authors: Jurica, M.S. / Monnat Jr., R.J. / Stoddard, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.3 KB | Display | ![]() |
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PDB format | ![]() | 128.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.2 KB | Display | ![]() |
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Full document | ![]() | 454.9 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1af5S 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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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 7418.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 24 BASE PAIR DUPLEX DNA #2: DNA chain | Mass: 7320.728 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 24 BASE PAIR DUPLEX DNA #3: Protein | Mass: 17516.121 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging 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 RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. all: 86360 / Num. obs: 86360 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.12 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.297 / % possible all: 79.6 |
Reflection | *PLUS Num. obs: 20643 / Num. measured all: 86360 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 79.6 % / Rmerge(I) obs: 0.297 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AF5 DIMER Resolution: 3→100 Å / Rfactor Rfree error: 0.0081 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3→100 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.14 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 100 Å / Rfactor obs: 0.242 / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3125 |