+Open data
-Basic information
Entry | Database: PDB / ID: 4z59 | ||||||
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Title | HipB-O4 20mer complex | ||||||
Components |
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Keywords | Transcription/DNA / HTH motif / Transcription repressor / HipA sequestering / Transcription-DNA complex | ||||||
Function / homology | Function and homology information toxin-antitoxin complex / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Min, J. / Brennan, R.G. / Schumacher, M.A. | ||||||
Citation | Journal: To be published Title: Molecular mechanism on hipBA gene regulation. Authors: Min, J. / Wang, A. / Brennan, R.G. / Schumacher, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z59.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z59.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 4z59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z59_validation.pdf.gz | 412.5 KB | Display | wwPDB validaton report |
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Full document | 4z59_full_validation.pdf.gz | 413.2 KB | Display | |
Data in XML | 4z59_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 4z59_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/4z59 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/4z59 | HTTPS FTP |
-Related structure data
Related structure data | 4z58C 4z5cC 4z5dC 4z5hC 4z52 4z56 4z57 4z5a 4z5b 4z5e 4z5f 4z5g 4z5i 4z5j 4z5k 4z5l 4z5m 4z5n 4z5o C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 8060.239 Da / Num. of mol.: 1 / Fragment: UNP residues 4-74 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hipB, b1508, JW1501 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS-T1 / References: UniProt: P23873 |
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#2: DNA chain | Mass: 6133.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1 M sodium citrate |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 7, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rigaku Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 16312 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.009 / Net I/av σ(I): 43.152 / Net I/σ(I): 11.5 / Num. measured all: 312178 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4Z52 4z52 Resolution: 2.3→45.032 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8997 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 15.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.74 Å2 / Biso mean: 23.5411 Å2 / Biso min: 4.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→45.032 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 16.9301 Å / Origin y: 42.6362 Å / Origin z: 14.7597 Å
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Refinement TLS group |
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