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Yorodumi- PDB-7trw: Crystal Structure of the C-terminal Ligand-Binding Domain of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7trw | ||||||
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Title | Crystal Structure of the C-terminal Ligand-Binding Domain of the LysR family Transcriptional Regulator YfbA from Yersinia pestis | ||||||
Components | LysR-family transcriptional regulatory protein | ||||||
Keywords | TRANSCRIPTION / LysR transcriptional regulator / solute binding domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pestis CO92 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å | ||||||
Authors | Kim, Y. / Tesar, C. / Crawford, M. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the C-terminal Ligand-Binding Domain of the LysR family Transcriptional Regulator YfbA from Yersinia pestis Authors: Kim, Y. / Tesar, C. / Crawford, M. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7trw.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7trw.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 7trw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7trw_validation.pdf.gz | 962.7 KB | Display | wwPDB validaton report |
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Full document | 7trw_full_validation.pdf.gz | 964 KB | Display | |
Data in XML | 7trw_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 7trw_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/7trw ftp://data.pdbj.org/pub/pdb/validation_reports/tr/7trw | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24016.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: lysR10, y2171, YP_1951 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: Q8D0G2 |
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#2: Chemical | ChemComp-3HB / |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 3.12 Å3/Da / Density % sol: 60.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.03 M Sodium/Potassium Phosphate, pH 5.0, 150 mM Malate, 3.0 % v/v PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 13379 / % possible obs: 99.9 % / Redundancy: 16.4 % / Biso Wilson estimate: 67.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.048 / Rrim(I) all: 0.203 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.28→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.366 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 655 / CC1/2: 0.388 / Rpim(I) all: 0.67 / Rrim(I) all: 1.54 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.28→37.27 Å / SU ML: 0.3585 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.561 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: 81.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→37.27 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 / Auth asym-ID: A / Label asym-ID: A
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