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Yorodumi- PDB-3hfu: Crystal structure of the ligand binding domain of E. coli CynR wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hfu | ||||||
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Title | Crystal structure of the ligand binding domain of E. coli CynR with its specific effector azide | ||||||
Components | HTH-type transcriptional regulator cynR | ||||||
Keywords | TRANSCRIPTION / CynR / LysR transcriptional activiator / effector / azide / Activator / Cytoplasm / DNA-binding / Repressor / Transcription regulation | ||||||
Function / homology | Function and homology information protein-DNA complex / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Singer, A.U. / Evdokimova, E. / Kagan, O. / Dong, A. / Edwards, A.M. / Savchenko, A. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of the ligand binding domain of E. coli CynR with its specific effector azide Authors: Singer, A.U. / Evdokimova, E. / Kagan, O. / Cuff, M.E. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hfu.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hfu.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/3hfu ftp://data.pdbj.org/pub/pdb/validation_reports/hf/3hfu | HTTPS FTP |
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-Related structure data
Related structure data | 2hxrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26405.803 Da / Num. of mol.: 4 / Fragment: UNP residues 63-299 Source method: isolated from a genetically manipulated source Details: TEV cleavage following purification / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0338, cynR, JW5894 / Plasmid: p15Tvlic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-Plus RP / References: UniProt: P27111 #2: Chemical | ChemComp-AZI / #3: Chemical | #4: 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: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG5000 monomethyl ether (MME) plus 100 mM Tris 8.5, cryoprotected in 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 8, 2006 / Details: mirrors |
Radiation | Monochromator: VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 44622 / Num. obs: 44532 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 55.588 Å2 / Rsym value: 0.111 / Net I/σ(I): 17.78 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 3.09 / Num. unique all: 4444 / % possible all: 99.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HXR Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 41.526 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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LS refinement shell | Resolution: 2.6→2.63 Å
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