+Open data
-Basic information
Entry | Database: PDB / ID: 2a8v | ||||||
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Title | RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX | ||||||
Components |
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Keywords | PROTEIN/RNA / RHO / OB FOLD / SINGLE-STRANDED NUCLEIC ACID BINDING DOMAIN / PROTEIN-RNA COMPLEX | ||||||
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 / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bogden, C.E. / Fass, D. / Bergman, N. / Nichols, M.D. / 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 | 2a8v.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a8v.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 2a8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/2a8v ftp://data.pdbj.org/pub/pdb/validation_reports/a8/2a8v | HTTPS FTP |
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-Related structure data
Related structure data | 1a8vSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: RNA chain | Mass: 870.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5A / Plasmid: PET24B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 | ||
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#2: RNA chain | Mass: 1786.133 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 13218.041 Da / Num. of mol.: 3 / Fragment: N-TERMINAL RNA BINDING DOMAIN Source method: isolated from a genetically manipulated source References: UniProt: P03002, UniProt: P0AG30*PLUS #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ / Method: vapor diffusion, hanging drop / pH: 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9779 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→14 Å / Num. obs: 14393 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.074 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.283 / % possible all: 99.6 |
Reflection | *PLUS Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.283 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A8V Resolution: 2.4→14 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→14 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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