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Open data
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Basic information
Entry | Database: PDB / ID: 6wp7 | ||||||
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Title | Avenolide Binding Autoregulator AvaR1 | ||||||
![]() | AvaR1 | ||||||
![]() | DNA BINDING PROTEIN / Transcriptional Repressor | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kapoor, I. / Olivares, P.J. / Nair, S.K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.9 KB | Display | ![]() |
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PDB format | ![]() | 145.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 27319.021 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680 Gene: avaR1, SAVERM_3705 / Plasmid: Rosetta Production host: ![]() ![]() References: UniProt: Q82H41 #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 10 % PEG 1000, 0.1M Sodium Citrate Tribasic Dihydrate pH 4.2, 0.2M Lithium sulfate, 4% v/v tert-butanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.27 Å / Num. obs: 64582 / % possible obs: 98.9 % / Redundancy: 2.58 % / CC1/2: 0.995 / Net I/σ(I): 7.62 |
Reflection shell | Resolution: 2.4→2.486 Å / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 3320 / % possible all: 99.96 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.76 Å2 / Biso mean: 52.803 Å2 / Biso min: 13.91 Å2
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Refinement step | Cycle: final / Resolution: 2.4→39.27 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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