+Open data
-Basic information
Entry | Database: PDB / ID: 7lza | |||||||||
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Title | Activated form of VanR from S. coelicolor | |||||||||
Components | Putative two-component system response regulatorTwo-component regulatory system | |||||||||
Keywords | TRANSCRIPTION / beryllium fluoride / antibiotic resistance / response regulator | |||||||||
Function / homology | Function and homology information phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / cytosol Similarity search - Function | |||||||||
Biological species | Streptomyces coelicolor (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å | |||||||||
Authors | Maciunas, L.J. / Loll, P.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Structures of full-length VanR from Streptomyces coelicolor in both the inactive and activated states. Authors: Maciunas, L.J. / Porter, N. / Lee, P.J. / Gupta, K. / Loll, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lza.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lza.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 7lza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/7lza ftp://data.pdbj.org/pub/pdb/validation_reports/lz/7lza | HTTPS FTP |
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-Related structure data
Related structure data | 7lz9C 1kgsS 5uicS 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: 24976.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria) Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO3590 / Plasmid: pETHSUL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8CJW1 |
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#2: Chemical | ChemComp-BEF / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.16 % / Description: rod |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7 Details: Protein stock (11.3 mg/mL in 500 mM NaCl, 5 mM MgCl2, 10% glycerol, 40 mM Tris pH 8) was mixed 10:1 (v/v) with 50 mM BeSO4, 350 mM NaF, and 70 mM MgCl2. 0.5 uL of this solution was mixed ...Details: Protein stock (11.3 mg/mL in 500 mM NaCl, 5 mM MgCl2, 10% glycerol, 40 mM Tris pH 8) was mixed 10:1 (v/v) with 50 mM BeSO4, 350 mM NaF, and 70 mM MgCl2. 0.5 uL of this solution was mixed with an equal volume of 2.5 M NaCl, 0.1 M Tris pH 7, 0.2 M MgCl2 and incubated under Al's Oil |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920091 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920091 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→28.85 Å / Num. obs: 21574 / % possible obs: 97.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.03→2.1 Å / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1981 / CC1/2: 0.916 / Rpim(I) all: 0.145 / Rrim(I) all: 0.463 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UIC, 1KGS Resolution: 2.03→28.85 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 95.37 Å2 / Biso mean: 41.4075 Å2 / Biso min: 23.48 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→28.85 Å
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LS refinement shell | Resolution: 2.03→2.12 Å
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