[English] 日本語
Yorodumi- PDB-7x2r: Crystal structure of the E. coli transcription termination factor Rho -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x2r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the E. coli transcription termination factor Rho | ||||||
Components | Transcription termination factor Rho | ||||||
Keywords | TRANSCRIPTION / E. coli transcription termination factor / TRANSLATION / HYDROLASE | ||||||
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 / RNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli 'BL21-GoldpLysS AG' | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å | ||||||
Authors | Zheng, J. / Wang, B. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: E. coli transcription termination factor Rho Authors: Wang, B. / Zheng, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7x2r.cif.gz | 579.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7x2r.ent.gz | 387.8 KB | Display | PDB format |
PDBx/mmJSON format | 7x2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x2r_validation.pdf.gz | 471.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7x2r_full_validation.pdf.gz | 526.4 KB | Display | |
Data in XML | 7x2r_validation.xml.gz | 87.3 KB | Display | |
Data in CIF | 7x2r_validation.cif.gz | 116 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/7x2r ftp://data.pdbj.org/pub/pdb/validation_reports/x2/7x2r | HTTPS FTP |
-Related structure data
Related structure data | 6xavS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 47070.168 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Gene: rho, NCTC10429_00403 / Production host: Escherichia coli (E. coli) References: UniProt: A0A377BS88, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % |
---|---|
Crystal grow | Temperature: 291.1 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.4 M potassium chloride, 0.05 M magnesium chloride, 50 mM Tris pH 7.5, 13% (w/v) polyethylene glycol (PEG) 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.988 Å |
Detector | Type: AGILENT EOS CCD / Detector: CCD / Date: Nov 1, 2017 |
Radiation | Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 4.4→20 Å / Num. obs: 170098 / % possible obs: 86 % / Redundancy: 5 % / Biso Wilson estimate: 43.88 Å2 / CC1/2: 0.8 / Net I/σ(I): 0.8 |
Reflection shell | Resolution: 4.4→4.53 Å / Num. unique obs: 7 / CC1/2: 0.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XAV Resolution: 4.4→19.99 Å / SU ML: 0.6051 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6191 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.4→19.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|