+Open data
-Basic information
Entry | Database: PDB / ID: 1jfs | ||||||
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Title | PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA-BINDING / REPRESSOR / PURINE BIOSYNTHESIS / COMPLEX (DNA-BINDING PROTEIN-DNA) / ALLOSTERIC REGULATION / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Huffman, J.L. / Lu, F. / Zalkin, H. / Brennan, R.G. | ||||||
Citation | Journal: Biochemistry / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jfs.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jfs.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jfs ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jfs | HTTPS FTP |
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-Related structure data
Related structure data | 1jftC 1jh9C 1jhzC 1pnrS S: Starting model for refinement C: citing same article (ref.) |
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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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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 |
-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.) Escherichia coli (E. coli) / Gene: PURR / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 LAMBDA DE3 / References: UniProt: P0ACP7 |
#3: Chemical | ChemComp-HPA / |
#4: 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: 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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