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Yorodumi- PDB-1sig: CRYSTAL STRUCTURE OF A SIGMA70 SUBUNIT FRAGMENT FROM ESCHERICHIA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sig | ||||||
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Title | CRYSTAL STRUCTURE OF A SIGMA70 SUBUNIT FRAGMENT FROM ESCHERICHIA COLI RNA POLYMERASE | ||||||
Components | RNA POLYMERASE PRIMARY SIGMA FACTOR | ||||||
Keywords | TRANSCRIPTION REGULATION / RNA POLYMERASE SIGMA FACTOR | ||||||
Function / homology | Function and homology information sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / response to heat / negative regulation of DNA-templated transcription / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MULTIWAVELENGTH ANOMALOUS DISPERSION / Resolution: 2.6 Å | ||||||
Authors | Malhotra, A. / Severinova, E. / Darst, S.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Authors: Malhotra, A. / Severinova, E. / Darst, S.A. #1: Journal: J.Mol.Biol. / Year: 1996 Title: Domain Organization of the Escherichia Coli RNA Polymerase Sigma 70 Subunit Authors: Severinova, E. / Severinov, K. / Fenyo, D. / Marr, M. / Brody, E.N. / Roberts, J.W. / Chait, B.T. / Darst, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sig.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sig.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 1sig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sig_validation.pdf.gz | 415.7 KB | Display | wwPDB validaton report |
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Full document | 1sig_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 1sig_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 1sig_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/1sig ftp://data.pdbj.org/pub/pdb/validation_reports/si/1sig | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39092.883 Da / Num. of mol.: 1 / Fragment: RESIDUES 114 - 448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: RPOD / Plasmid: PET15B (NOVAGEN) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): RPOD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00579 |
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#2: 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: 2.7 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.1 Details: PROTEIN CRYSTALLIZED FROM 50 MM SODIUM ACETATE, 0.5-0.7 M LI2SO4, 5-7% (W/V) PEG 8000, 5 MM DTT, PH 5.1; TRANSFERRED IN EIGHT STEPS TO 50 MM SODIUM ACETATE, 0.5 M LI2SO4, 15% (W/V) PEG 8000, ...Details: PROTEIN CRYSTALLIZED FROM 50 MM SODIUM ACETATE, 0.5-0.7 M LI2SO4, 5-7% (W/V) PEG 8000, 5 MM DTT, PH 5.1; TRANSFERRED IN EIGHT STEPS TO 50 MM SODIUM ACETATE, 0.5 M LI2SO4, 15% (W/V) PEG 8000, 17.5% GLYCEROL AND 10MM DTT, PH 5.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / Details: Severinova, E., (1996) J.Mol.Biol., 263, 637. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9663 / Wavelength: 0.9663, 0.9879 | |||||||||
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Aug 25, 1995 / Details: COLLIMATOR | |||||||||
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→15 Å / Num. obs: 13160 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.84 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.063 / Net I/σ(I): 15.1 | |||||||||
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 4.63 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.27 / % possible all: 78.3 | |||||||||
Reflection | *PLUS Num. measured all: 76887 / Rmerge(I) obs: 0.063 | |||||||||
Reflection shell | *PLUS % possible obs: 78.3 % / Rmerge(I) obs: 0.27 |
-Processing
Software |
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Refinement | Method to determine structure: MULTIWAVELENGTH ANOMALOUS DISPERSION Resolution: 2.6→6 Å / Rfactor Rfree error: 0.0092 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 49.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.71 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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