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Open data
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Basic information
Entry | Database: PDB / ID: 1jfs | ||||||
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Title | PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX | ||||||
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![]() | TRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA-BINDING / REPRESSOR / PURINE BIOSYNTHESIS / COMPLEX (DNA-BINDING PROTEIN-DNA) / ALLOSTERIC REGULATION / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() guanine binding / negative regulation of purine nucleotide biosynthetic process / purine nucleotide biosynthetic process / DNA-binding transcription repressor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Huffman, J.L. / Lu, F. / Zalkin, H. / Brennan, R.G. | ||||||
![]() | ![]() Title: Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor. Authors: Huffman, J.L. / Lu, F. / Zalkin, H. / Brennan, R.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.9 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 392.9 KB | Display | ![]() |
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Full document | ![]() | 424.8 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jftC ![]() 1jh9C ![]() 1jhzC ![]() 1pnrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is a protein homodimer and duplex oligonucleotide, generated from the protein monomer and single DNA strand in the asymmetric unit by applying the following to chains A, B: 1 1.000000 0.000000 0.000000 0.00000 1 0.000000 1.000000 0.000000 0.00000 1 0.000000 0.000000 1.000000 0.00000 2 1.000000 0.000000 0.000000 0.00000 2 0.000000 -1.000000 0.000000 0.00000 2 0.000000 0.000000 -1.000000 0.00000 |
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Components
#1: DNA chain | Mass: 5202.384 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 38052.559 Da / Num. of mol.: 1 / Mutation: W147F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-HPA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.64 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, ammonium phosphate, ammonium sulfate, cobalt hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: UCSD MARK III / Detector: AREA DETECTOR / Date: Oct 16, 1996 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→10 Å / Num. all: 28721 / Num. obs: 28721 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 34.49 Å2 / Rsym value: 7.54 / Net I/σ(I): 4.84 |
Reflection shell | Resolution: 2.9→3.11 Å / Redundancy: 5.28 % / Mean I/σ(I) obs: 1.35 / Num. unique all: 15190 / Rsym value: 20 / % possible all: 97.7 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 13773 / Num. measured all: 28721 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS Lowest resolution: 3.12 Å / % possible obs: 97.7 % / Rmerge(I) obs: 0.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PNR Resolution: 2.9→10 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 47.263 Å2 / ksol: 0.5412 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 4.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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