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Yorodumi- PDB-1lb2: Structure of the E. coli alpha C-terminal domain of RNA polymeras... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lb2 | ||||||
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Title | Structure of the E. coli alpha C-terminal domain of RNA polymerase in complex with CAP and DNA | ||||||
Components |
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Keywords | GENE REGULATION/DNA / PROTEIN-DNA COMPLEX / GENE-REGULATORY / GENE REGULATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information carbon catabolite repression of transcription / DNA binding, bending / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / minor groove of adenine-thymine-rich DNA binding / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...carbon catabolite repression of transcription / DNA binding, bending / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / minor groove of adenine-thymine-rich DNA binding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / cAMP binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / protein-DNA complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / sequence-specific DNA binding / intracellular iron ion homeostasis / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, FOURIER SYNTHESIS / Resolution: 3.1 Å | ||||||
Authors | Benoff, B. / Yang, H. / Lawson, C.L. / Parkinson, G. / Liu, J. / Blatter, E. / Ebright, Y.W. / Berman, H.M. / Ebright, R.H. | ||||||
Citation | Journal: Science / Year: 2002 Title: Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Authors: Benoff, B. / Yang, H. / Lawson, C.L. / Parkinson, G. / Liu, J. / Blatter, E. / Ebright, Y.W. / Berman, H.M. / Ebright, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lb2.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lb2.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lb2_validation.pdf.gz | 775.6 KB | Display | wwPDB validaton report |
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Full document | 1lb2_full_validation.pdf.gz | 799.2 KB | Display | |
Data in XML | 1lb2_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1lb2_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/1lb2 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/1lb2 | HTTPS FTP |
-Related structure data
Related structure data | 2cgpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules KJ
#1: DNA chain | Mass: 6088.962 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 7409.844 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 2 types, 3 molecules ABE
#3: Protein | Mass: 23541.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACJ8 |
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#4: Protein | Mass: 9364.795 Da / Num. of mol.: 2 / Fragment: alpha CTD, alpha Carboxy terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase |
-Non-polymers , 2 types, 33 molecules
#5: Chemical | ChemComp-CMP / |
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#6: 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: 6 Å3/Da / Density % sol: 78 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: NaCl, NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jul 6, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. all: 23331 / Num. obs: 23331 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.3 % / Biso Wilson estimate: 81.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 1.5 / % possible all: 38.5 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 88 % / Num. measured all: 332877 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, FOURIER SYNTHESIS Starting model: 2CGP Resolution: 3.1→20 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 47.7314 Å2 / ksol: 0.272486 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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