+Open data
-Basic information
Entry | Database: PDB / ID: 6wpa | ||||||
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Title | Structure of AvaR1 bound to DNA half-site | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Transcriptional Repressor / DNA oligonucleotide / DNA-Protein biniding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avermitilis (bacteria) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å | ||||||
Authors | Kapoor, I. / Olivares, P.J. / Nair, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 Title: Biochemical basis for the regulation of biosynthesis of antiparasitics by bacterial hormones. Authors: Kapoor, I. / Olivares, P. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wpa.cif.gz | 366.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wpa.ent.gz | 292.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wpa_validation.pdf.gz | 500.8 KB | Display | wwPDB validaton report |
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Full document | 6wpa_full_validation.pdf.gz | 520.7 KB | Display | |
Data in XML | 6wpa_validation.xml.gz | 56.3 KB | Display | |
Data in CIF | 6wpa_validation.cif.gz | 76.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/6wpa ftp://data.pdbj.org/pub/pdb/validation_reports/wp/6wpa | HTTPS FTP |
-Related structure data
Related structure data | 6wp7SC 6wp9C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27037.654 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: AvaR1 bound to DNA oligonucleotide through its DNA binding domain Source: (gene. exp.) Streptomyces avermitilis (bacteria) Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680 Gene: avaR1, SAVERM_3705 / Plasmid: Rosetta Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q82H41 #2: DNA chain | Mass: 8604.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Palindromic double stranded DNA (28-MER) Source: (synth.) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Potassium chloride, 0.01 M Magnesium chloride hexahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.5, 10% w/v Polyethylene glycol 4000 with additive 40 % Formamide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→25 Å / Num. obs: 55544 / % possible obs: 100 % / Redundancy: 15.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.021 / Rrim(I) all: 0.079 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 3.09→3.2 Å / Num. unique obs: 5510 / CC1/2: 0.999 / Rpim(I) all: 0.338 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WP7 Resolution: 3.09→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.645 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 213.84 Å2 / Biso mean: 106.635 Å2 / Biso min: 48.06 Å2
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Refinement step | Cycle: final / Resolution: 3.09→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.09→3.165 Å / Rfactor Rfree error: 0
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