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Open data
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Basic information
Entry | Database: PDB / ID: 6jg9 | ||||||
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Title | Crystal structure of AimR in complex with arbitrium peptide | ||||||
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![]() | PEPTIDE BINDING PROTEIN/PEPTIDE / AimR / Apo / HTH / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-PEPTIDE complex | ||||||
Function / homology | : / latency-replication decision / AimR transcriptional regulator![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guan, Z.Y. / Pei, K. / Zou, T.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.1 KB | Display | ![]() |
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PDB format | ![]() | 275.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.5 KB | Display | ![]() |
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Full document | ![]() | 480.8 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jg5C ![]() 6jg8C ![]() 5xybS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 588.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |