+Open data
-Basic information
Entry | Database: PDB / ID: 1jh9 | ||||||
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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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 | 1jh9.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jh9.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/1jh9 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/1jh9 | HTTPS FTP |
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-Related structure data
Related structure data | 1jfsC 1jftC 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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-Components
#1: DNA chain | Mass: 5210.410 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: Protein | Mass: 38062.578 Da / Num. of mol.: 1 / Mutation: W147R 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 | #4: Chemical | ChemComp-HPA / | #5: 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: 3.77 Å3/Da / Density % sol: 67.33 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, ammonium sulfate, ammonium phosphate, cobalt hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
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: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998 |
Radiation | Monochromator: HORIZONTAL FOCUS SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.55 Å / Num. all: 22093 / Num. obs: 22093 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 4.89 |
Reflection shell | Resolution: 2.55→2.61 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1612 / % possible all: 99.8 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PNR Resolution: 2.55→10 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 4.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→10 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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