+Open data
-Basic information
Entry | Database: PDB / ID: 6jg9 | ||||||
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Title | Crystal structure of AimR in complex with arbitrium peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN/PEPTIDE / AimR / Apo / HTH / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-PEPTIDE complex | ||||||
Function / homology | : / latency-replication decision / AimR transcriptional regulator Function and homology information | ||||||
Biological species | Bacillus phage SPbeta (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å | ||||||
Authors | Guan, Z.Y. / Pei, K. / Zou, T.T. | ||||||
Citation | Journal: Cell Discov / Year: 2019 Title: Structural insights into DNA recognition by AimR of the arbitrium communication system in the SPbeta phage. Authors: Guan, Z.Y. / Pei, K. / Wang, J. / Cui, Y.Q. / Zhu, X. / Su, X. / Zhou, Y.B. / Zhang, D.L. / Tang, C. / Yin, P. / Liu, Z. / Zou, T.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jg9.cif.gz | 337.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jg9.ent.gz | 275.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jg9_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 6jg9_full_validation.pdf.gz | 480.8 KB | Display | |
Data in XML | 6jg9_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 6jg9_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/6jg9 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/6jg9 | HTTPS FTP |
-Related structure data
Related structure data | 6jg5C 6jg8C 5xybS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 46575.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage SPbeta (virus) / Gene: aimR, yopK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O64094 #2: Protein/peptide | Mass: 588.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus phage SPbeta (virus) #3: 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: 2.32 Å3/Da / Density % sol: 47.04 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: sodium cacodylate, PEG 8000, NaBr, DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.123 Å / Num. obs: 60685 / % possible obs: 100 % / Redundancy: 25.7 % / Net I/σ(I): 39.1 |
Reflection shell | Resolution: 2→2.07 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XYB Resolution: 1.998→46.123 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.68 / 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: 1.998→46.123 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.5016 Å / Origin y: 42.5346 Å / Origin z: 14.3026 Å
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Refinement TLS group | Selection details: all |