+Open data
-Basic information
Entry | Database: PDB / ID: 2iu5 | ||||||
---|---|---|---|---|---|---|---|
Title | Dihydroxyacetone kinase operon activator DhaS | ||||||
Components | HTH-TYPE DHAKLM OPERON TRANSCRIPTIONAL ACTIVATOR DHAS | ||||||
Keywords | TRANSCRIPTION / SYNTHASE / ACTIVATOR / TETR FAMILY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LACTOCOCCUS LACTIS SUBSP. LACTIS IL1403 (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.6 Å | ||||||
Authors | Srinivas, A. / Christen, S. / Baumann, U. / Erni, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Regulation of the Dha Operon of Lactococcus Lactis: A Deviation from the Rule Followed by the Tetr Family of Transcription Regulators Authors: Christen, S. / Srinivas, A. / Bahler, P. / Zeller, A. / Pridmore, D. / Bieniossek, C. / Baumann, U. / Erni, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2iu5.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2iu5.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 2iu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2iu5 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2iu5 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 23574.805 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. LACTIS IL1403 (lactic acid bacteria) Description: NESTLE / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CIV9 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | SECOND AMINO ACID IS MODIFIED TO GLUTAMATE FROM LYSINE AND THE C-TERMINAL HAS EIGHT ADDITIONAL ...SECOND AMINO ACID IS MODIFIED TO GLUTAMATE FROM LYSINE AND THE C-TERMINAL HAS EIGHT ADDITIONAL | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34.64 % |
---|---|
Crystal grow | pH: 6 Details: THE CONCENTRATED PROTEIN (20 MG/ML) WAS MIXED WITH BUFFER CONTAINING 50 MM NA-CACODYLATE PH 6.0, 1.7 M AMMONIUM SULFATE, 0.015 M MG-ACETATE IN A 1:1 RATIO. |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 45492 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 0.07 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.502 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|