+Open data
-Basic information
Entry | Database: PDB / ID: 1tzt | ||||||
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Title | T. maritima NusB, P21 | ||||||
Components | N utilization substance protein B homolog | ||||||
Keywords | TRANSCRIPTION / N-utilization substance / NusB / RNA-protein interaction / transcriptional antitermination / transcription regulation | ||||||
Function / homology | Function and homology information transcription antitermination / DNA-templated transcription termination / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Bonin, I. / Robelek, R. / Benecke, H. / Urlaub, H. / Bacher, A. / Richter, G. / Wahl, M.C. | ||||||
Citation | Journal: Biochem.J. / Year: 2004 Title: Crystal structures of the antitermination factor NusB from Thermotoga maritima and implications for RNA binding Authors: Bonin, I. / Robelek, R. / Benecke, H. / Urlaub, H. / Bacher, A. / Richter, G. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tzt.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tzt.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tzt_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 1tzt_full_validation.pdf.gz | 449.5 KB | Display | |
Data in XML | 1tzt_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 1tzt_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/1tzt ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tzt | HTTPS FTP |
-Related structure data
Related structure data | 1tzuC 1tzvC 1tzwC 1tzxC 1eyvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17003.572 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nusb, TM1765 / Plasmid: pNCO113, pNOC113-tmanusb / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9X286 #2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: ammonium sulfate, PEG 8000, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 1, 2002 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.616 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1EYV Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.021 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE WAS REFINED ALSO WITH CNS 1.0.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.632 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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