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Yorodumi- PDB-1d8l: E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d8l | ||||||
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Title | E. COLI HOLLIDAY JUNCTION BINDING PROTEIN RUVA NH2 REGION LACKING DOMAIN III | ||||||
Components | PROTEIN (HOLLIDAY JUNCTION DNA HELICASE RUVA) | ||||||
Keywords | GENE REGULATION / OB-FOLD / HELIX-HAIRPIN-HELIX MOTIF | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Nishino, T. / Iwasaki, H. / Kataoka, M. / Ariyoshi, M. / Fujita, T. / Shinagawa, H. / Morikawa, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d8l.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d8l.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1d8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/1d8l ftp://data.pdbj.org/pub/pdb/validation_reports/d8/1d8l | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-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.) Escherichia coli (E. coli) / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A809 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
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 |
-Processing
Software |
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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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