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Yorodumi- PDB-7t8i: Crystal structure of the ImmR transcriptional regulator DNA-bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t8i | ||||||
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Title | Crystal structure of the ImmR transcriptional regulator DNA-binding domain of Bacillus subtilis | ||||||
Components | (Phage element (ICEBs1)transcriptional regulator (Xre family)) x 2 | ||||||
Keywords | DNA BINDING PROTEIN / HTH-DNA binding domain / dimerisation / immunity repressor protein / bacterial infection / horizontal gene transfer | ||||||
Function / homology | Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Phage element (ICEBs1)transcriptional regulator (Xre family) Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Caliandro, R. / de Diego, I. / Gomis-Ruth, F.X. | ||||||
Funding support | 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Crystal structure report of the ImmR transcriptional regulator DNA-binding domain of the Bacillus subtilis ICEBs1 transposon. Authors: Caliandro, R. / de Diego, I. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t8i.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t8i.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 7t8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t8i_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 7t8i_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 7t8i_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 7t8i_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/7t8i ftp://data.pdbj.org/pub/pdb/validation_reports/t8/7t8i | 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 oper: (Code: givenMatrix: (-0.999954986145, -0.00901027934436, -0.00297330607399), (0.00901936055168, -0.999954657711, -0.00305510351193), (-0.00294564392142, -0.00308178330946, 0.999990912855) ...NCS oper: (Code: given Matrix: (-0.999954986145, -0.00901027934436, -0.00297330607399), Vector: |
-Components
#1: Protein | Mass: 7505.378 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues G-A are left over from the expression tag. Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_4397, SC09_Contig25orf00616 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1M9H4 |
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#2: Protein | Mass: 7492.360 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues G-A are left over from the expression tag. Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_4397, SC09_Contig25orf00616 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1M9H4 |
#3: 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: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Suitable crystals of ImmR-DBD were obtained with 18%(w) PEG 3350, 10 mM magnesium chloride, 50 mM Tris-HCl pH 8.5 as reservoir solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.97 Å / Num. obs: 9322 / % possible obs: 94 % / Redundancy: 2.8 % / Biso Wilson estimate: 5.8 Å2 / CC1/2: 0.904 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.186 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.617 / Num. unique obs: 464 / CC1/2: 0.591 / Rpim(I) all: 0.433 / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold model Resolution: 2.1→43.97 Å / SU ML: 0.4141 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.136 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→43.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.786370242233 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 0 - 64 / Label seq-ID: 1 - 65
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