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Yorodumi- PDB-5ztc: Apo structure of TetR family transcription regulator Lmo2088 of L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ztc | ||||||
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Title | Apo structure of TetR family transcription regulator Lmo2088 of Listeria monocytogenes EGDe | ||||||
Components | Lmo2088 protein | ||||||
Keywords | TRANSCRIPTION / TetR family | ||||||
Function / homology | Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / Lmo2088 protein Function and homology information | ||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Samad, A. / Jin, T. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: X-ray crystal structure of putative transcription regulator lmo2088 from Listeria monocytogenes. Authors: Samad, A. / Li, Y. / Zhang, C. / Chen, F. / Zeng, W. / Fan, X. / Jin, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ztc.cif.gz | 178.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ztc.ent.gz | 142.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ztc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/5ztc ftp://data.pdbj.org/pub/pdb/validation_reports/zt/5ztc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23938.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo2088 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y5H4 #2: Chemical | #3: 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: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Sodium citrate pH 5.0, 30 % Jeffammine ED2001 pH 7.0 PH range: 5.0-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 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: 1.7→50 Å / Num. obs: 55811 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.097 / Net I/σ(I): 9.81 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4.45 % / Mean I/σ(I) obs: 2.28 / Num. unique obs: 8969 / CC1/2: 0.917 / Rrim(I) all: 0.633 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→36.613 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.81 / 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: 1.7→36.613 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: 23.3549 Å / Origin y: 34.1092 Å / Origin z: 16.5485 Å
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Refinement TLS group | Selection details: all |