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- PDB-1d8l: E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d8l | ||||||
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Title | E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING DOMAIN III | ||||||
![]() | PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA) | ||||||
![]() | GENE REGULATION / OB-FOLD / HELIX-HAIRPIN-HELIX MOTIF | ||||||
Function / homology | ![]() Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / recombinational repair / SOS response / four-way junction DNA binding / response to radiation / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Nishino, T. / Iwasaki, H. / Kataoka, M. / Ariyoshi, M. / Fujita, T. / Shinagawa, H. / Morikawa, K. | ||||||
![]() | ![]() Title: Modulation of RuvB function by the mobile domain III of the Holliday junction recognition protein RuvA. Authors: Nishino, T. / Iwasaki, H. / Kataoka, M. / Ariyoshi, M. / Fujita, T. / Shinagawa, H. / Morikawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64 KB | Display | ![]() |
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PDB format | ![]() | 48.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429 KB | Display | ![]() |
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Full document | ![]() | 437.6 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Components
#1: Protein | Mass: 16499.352 Da / Num. of mol.: 2 / Fragment: NH2 REGION Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.28 % | ||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.60 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.6 / Method: microdialysis | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Jan 22, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 10073 / % possible obs: 85.6 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.3 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 15 Å / Num. obs: 9523 / Observed criterion σ(I): 1 / Redundancy: 5 % / Num. measured all: 49960 / Biso Wilson estimate: 57 Å2 |
Reflection shell | *PLUS % possible obs: 79.3 % / Rmerge(I) obs: 0.309 |
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Processing
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Refinement | Resolution: 2.5→15 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.243 / Rfactor Rfree: 0.32 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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