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Yorodumi- PDB-1a8v: STRUCTURE OF THE RNA-BINDING DOMAIN OF THE RHO TRANSCRIPTION TERM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a8v | ||||||
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Title | STRUCTURE OF THE RNA-BINDING DOMAIN OF THE RHO TRANSCRIPTION TERMINATOR | ||||||
Components | TRANSCRIPTION TERMINATION FACTOR RHO | ||||||
Keywords | TRANSCRIPTION TERMINATION / RNA-BINDING / TERMINATOR / RHO PROTEIN | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 Å | ||||||
Authors | Fass, D. / Bogden, C. / Berger, J.M. | ||||||
Citation | Journal: Mol.Cell / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a8v.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a8v.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a8v_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 1a8v_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 1a8v_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1a8v_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/1a8v ftp://data.pdbj.org/pub/pdb/validation_reports/a8/1a8v | HTTPS FTP |
-Related structure data
-Links
-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: |
-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.) Escherichia coli (E. coli) / Strain: DH5-ALPHA / Cell line: BL21 / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P03002, UniProt: P0AG30*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→20 Å / σ(F): 0 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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