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Yorodumi- PDB-3lhe: The crystal structure of the C-terminal domain of a GntR family t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lhe | ||||||
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Title | The crystal structure of the C-terminal domain of a GntR family transcriptional regulator from Bacillus anthracis str. Sterne | ||||||
Components | GntR family Transcriptional regulator | ||||||
Keywords | transcription regulator / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCS G / DNA-binding / Transcription / Transcription regulation / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å | ||||||
Authors | Tan, K. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the C-terminal domain of a GntR family transcriptional regulator from Bacillus anthracis str. Sterne Authors: Tan, K. / Chhor, G. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lhe.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lhe.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lhe_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 3lhe_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 3lhe_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3lhe_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/3lhe ftp://data.pdbj.org/pub/pdb/validation_reports/lh/3lhe | 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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Details | Experimentally unknown. The chain A seems to be monomeric. |
-Components
#1: Protein | Mass: 16439.135 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS3204, BA_3458, GBAA3458, GBAA_3458 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q81MW2, UniProt: A0A6L8PH04*PLUS | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.05 M Bis-Tris, 45% v/v PPGP 400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 19, 2009 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→26.1 Å / Num. all: 20951 / Num. obs: 20951 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 32.1 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 987 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.62→26.1 Å / SU ML: 0.19 / σ(F): 0 / 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 / Bsol: 60.24 Å2 / ksol: 0.413 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→26.1 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: 14.2269 Å / Origin y: 28.4184 Å / Origin z: 10.385 Å
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Refinement TLS group | Selection details: chain A |