+Open data
-Basic information
Entry | Database: PDB / ID: 8j6w | ||||||
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Title | Full length crystal structure of Escherichia coli Fur | ||||||
Components | Ferric uptake regulation protein | ||||||
Keywords | DNA BINDING PROTEIN / ferric uptake regulator | ||||||
Function / homology | Function and homology information negative regulation of siderophore biosynthetic process / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | ||||||
Authors | Zhang, F. / Wang, X. / Gu, L. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Full length crystal structure of Escherichia coli Fur Authors: Zhang, F. / Wang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j6w.cif.gz | 43.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j6w.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 8j6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/8j6w ftp://data.pdbj.org/pub/pdb/validation_reports/j6/8j6w | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 16823.893 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: fur, b0683, JW0669 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9A9 | ||||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.85 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 0.2M Potassium chloride,0.01M Magnesium chloride hexahydrate,0.05M MSA monohydrate,5%w/vPolyethylene glycol,pH=5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→32.38 Å / Num. obs: 5436 / % possible obs: 99.6 % / Redundancy: 1 % / Biso Wilson estimate: 64.79 Å2 / CC1/2: 0.995 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2.66→2.79 Å / Mean I/σ(I) obs: 6.7 / Num. unique obs: 690 / CC1/2: 0.995 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→32.38 Å / SU ML: 0.3862 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.2284 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.66→32.38 Å
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Refine LS restraints |
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LS refinement shell |
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