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- PDB-1a8v: STRUCTURE OF THE RNA-BINDING DOMAIN OF THE RHO TRANSCRIPTION TERM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1a8v | ||||||
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Title | STRUCTURE OF THE RNA-BINDING DOMAIN OF THE RHO TRANSCRIPTION TERMINATOR | ||||||
![]() | TRANSCRIPTION TERMINATION FACTOR RHO | ||||||
![]() | TRANSCRIPTION TERMINATION / RNA-BINDING / TERMINATOR / RHO PROTEIN | ||||||
Function / homology | ![]() ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fass, D. / Bogden, C. / Berger, J.M. | ||||||
![]() | ![]() Title: The structural basis for terminator recognition by the Rho transcription termination factor. Authors: Bogden, C.E. / Fass, D. / Bergman, N. / Nichols, M.D. / Berger, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.5 KB | Display | ![]() |
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PDB format | ![]() | 43.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.6 KB | Display | ![]() |
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Full document | ![]() | 442.3 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9995, 0.02591, 0.018), Vector: |
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Components
#1: Protein | Mass: 13544.437 Da / Num. of mol.: 2 / Fragment: RNA-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 14432 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 7 / % possible all: 95.8 |
Reflection shell | *PLUS % possible obs: 95.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Details: REFINEMENT WAS STARED USING WITH X-PLOR, TO A FREE-R FACTOR OF 36%. THE MODEL WAS REBUILT INTO SA-OMIT MAPS, THEN MOVED TO REFMAC/ARP FOR THE FINAL REFINEMENT ROUND. THE FREE-R SET WAS HELD ...Details: REFINEMENT WAS STARED USING WITH X-PLOR, TO A FREE-R FACTOR OF 36%. THE MODEL WAS REBUILT INTO SA-OMIT MAPS, THEN MOVED TO REFMAC/ARP FOR THE FINAL REFINEMENT ROUND. THE FREE-R SET WAS HELD CONSTANT THROUGHOUT THE REFINEMENT. BOND ANGLES (DEGREES) : 1.5
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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