+Open data
-Basic information
Entry | Database: PDB / ID: 6ipx | ||||||
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Title | Crystal structure of the apo form transcription factor | ||||||
Components | AimR transcriptional regulator | ||||||
Keywords | TRANSCRIPTION REGULATOR / a Virus protein / VIRUS | ||||||
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: 2.634 Å | ||||||
Authors | Oy, S.Y. / Zhen, X. / Zhou, H. / Ding, W. | ||||||
Citation | Journal: Protein Cell / Year: 2019 Title: Structural basis of AimP signaling molecule recognition by AimR in Spbeta group of bacteriophages. Authors: Zhen, X. / Zhou, H. / Ding, W. / Zhou, B. / Xu, X. / Perculija, V. / Chen, C.J. / Chang, M.X. / Choudhary, M.I. / Ouyang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ipx.cif.gz | 315.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ipx.ent.gz | 261.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ipx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ipx_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 6ipx_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 6ipx_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 6ipx_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ipx ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ipx | HTTPS FTP |
-Related structure data
Related structure data | 6im4C 6im2 C: citing same article (ref.) S: Starting model for refinement |
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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: 45849.477 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) / Strain (production host): BL21(DE3) / References: UniProt: O64094 |
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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: 2.38 Å3/Da / Density % sol: 48.24 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 4K, 50 mM magnesium acetate / Temp details: 289.15K |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97981 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97981 Å / Relative weight: 1 |
Reflection | Resolution: 2.634→107.355 Å / Num. obs: 49620 / % possible obs: 99.22 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.63→2.7 Å / Rmerge(I) obs: 0.075 / Num. unique obs: 1866 / CC1/2: 0.997 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IM2 6im2 Resolution: 2.634→107.355 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 0 / Phase error: 31.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.634→107.355 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.634 Å /
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Refinement TLS params. | Method: refined / Origin x: 29.7604 Å / Origin y: 29.0402 Å / Origin z: 44.0181 Å
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Refinement TLS group | Selection details: all |