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Yorodumi- PDB-6jyi: Crystal structure of the PadR-like transcriptional regulator BC17... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jyi | ||||||
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Title | Crystal structure of the PadR-like transcriptional regulator BC1756 from Bacillus cereus | ||||||
Components | Transcriptional repressor PadR | ||||||
Keywords | TRANSCRIPTION / Transcription factor | ||||||
Function / homology | Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Transcriptional repressor PadR Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å | ||||||
Authors | Kim, T.H. / Park, S.C. / Lee, K.C. / Song, W.S. / Yoon, S.I. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Structural and DNA-binding studies of the PadR-like transcriptional regulator BC1756 from Bacillus cereus. Authors: Kim, T.H. / Park, S.C. / Lee, K.C. / Song, W.S. / Yoon, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jyi.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jyi.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jyi_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 6jyi_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 6jyi_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 6jyi_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/6jyi ftp://data.pdbj.org/pub/pdb/validation_reports/jy/6jyi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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: 22197.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria) Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: BC_1756 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81F45 #2: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG 3350, sodium citrate, ammonium dihydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97939 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97939 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→30 Å / Num. obs: 31084 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 43.9 |
Reflection shell | Resolution: 1.92→1.99 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3033 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.845 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.9 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→30 Å
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Refine LS restraints |
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