+Open data
-Basic information
Entry | Database: PDB / ID: 7cv2 | ||||||
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Title | Crystal structure of B. halodurans NiaR in niacin-bound form | ||||||
Components | Transcriptional regulator NiaR | ||||||
Keywords | STRUCTURAL PROTEIN / NiaR / transcription factor / TRANSCTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å | ||||||
Authors | Lee, J.Y. / Lee, D.W. / Park, Y.W. / Lee, M.Y. / Jeong, K.H. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Structural analysis and insight into effector binding of the niacin-responsive repressor NiaR from Bacillus halodurans. Authors: Lee, D.W. / Park, Y.W. / Lee, M.Y. / Jeong, K.H. / Lee, J.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cv2.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cv2.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 7cv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cv2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7cv2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7cv2_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 7cv2_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/7cv2 ftp://data.pdbj.org/pub/pdb/validation_reports/cv/7cv2 | HTTPS FTP |
-Related structure data
Related structure data | 7cv0C 1j5yS 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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Unit cell |
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-Components
#1: Protein | Mass: 19920.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria) Gene: BH1216 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KDJ7 |
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#2: Chemical | ChemComp-NIO / |
#3: Chemical | ChemComp-ZN / |
#4: 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: 1.97 Å3/Da / Density % sol: 37.73 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: M Bis-Tris pH 8.5, PEG 6000, niacin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97941 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97941 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 15404 / % possible obs: 97.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 20.026 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 5.98 / Num. unique obs: 783 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J5Y Resolution: 1.802→18.786 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.802→18.786 Å
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Refine LS restraints |
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LS refinement shell |
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