+Open data
-Basic information
Entry | Database: PDB / ID: 7wjp | ||||||
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Title | Structure of PadR-like protein from Listeria monocytogenes | ||||||
Components | PadR family transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / listeria monocytogenes / Transcription factor / regulation / PadR | ||||||
Function / homology | Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / PadR family transcriptional regulator Function and homology information | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Hong, M. / Kim, J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Structure-based molecular characterization of the LltR transcription factor from Listeria monocytogenes. Authors: Kim, J. / Park, J. / Choi, Z. / Hong, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wjp.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wjp.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wjp_validation.pdf.gz | 429.6 KB | Display | wwPDB validaton report |
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Full document | 7wjp_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 7wjp_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 7wjp_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/7wjp ftp://data.pdbj.org/pub/pdb/validation_reports/wj/7wjp | HTTPS FTP |
-Related structure data
Related structure data | 5zqhS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 12714.470 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D2INR9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1 M lithium chloride, 0.1 M MES, pH 6.5, 17% polyethylene glycol 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 6256 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 49.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 56.6 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.25 / Num. unique obs: 188 / CC1/2: 0.983 / CC star: 0.997 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZQH Resolution: 2.25→36.09 Å / SU ML: 0.1646 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.9989 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: 65.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→36.09 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 |
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