+Open data
-Basic information
Entry | Database: PDB / ID: 7t5w | ||||||
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Title | Structure of E. coli CapH C-terminal domain | ||||||
Components | Helix-turn-helix domain-containing protein | ||||||
Keywords | DNA BINDING PROTEIN / helix turn helix / HTH / DdrO | ||||||
Function / homology | Helix-turn-helix domain / 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 transcription factor activity / DNA binding / cytosol / Helix-turn-helix domain-containing protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Lau, R.K. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Embo J. / Year: 2022 Title: A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage. Authors: Lau, R.K. / Enustun, E. / Gu, Y. / Nguyen, J.V. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t5w.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t5w.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 7t5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t5w_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 7t5w_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 7t5w_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 7t5w_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/7t5w ftp://data.pdbj.org/pub/pdb/validation_reports/t5/7t5w | HTTPS FTP |
-Related structure data
Related structure data | 7t5tC 7t5uC 7t5vSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/867 / Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/867 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5277.855 Da / Num. of mol.: 4 / Fragment: C-terminal residues 67-107 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: nadR_1, BHS87_27750, D9K17_19515, GRQ19_13110, HV109_14215, NCTC13216_00230 Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X1LKI5 #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: 1.9 Å3/Da / Density % sol: 35.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium Citrate pH 3.0, 1.6 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→100 Å / Num. obs: 15936 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.13 Å2 / CC1/2: 1 / Rpim(I) all: 0.039 / Rrim(I) all: 0.07 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 768 / CC1/2: 0.631 / Rpim(I) all: 0.45 / Rrim(I) all: 0.784 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7T5V Resolution: 1.75→45.72 Å / SU ML: 0.2478 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.585 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: 37.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→45.72 Å
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Refine LS restraints |
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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
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