+Open data
-Basic information
Entry | Database: PDB / ID: 2iu4 | ||||||
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Title | Dihydroxyacetone kinase operon co-activator Dha-DhaQ | ||||||
Components | DIHYDROXYACETONE KINASE | ||||||
Keywords | TRANSFERASE / LACTOCOCCUS LACTIS / DIHYDROXYACETONE / CO-ACTIVATOR / KINASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LACTOCOCCUS LACTIS (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iu4.cif.gz | 139.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iu4.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 2iu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iu4_validation.pdf.gz | 451.2 KB | Display | wwPDB validaton report |
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Full document | 2iu4_full_validation.pdf.gz | 463.6 KB | Display | |
Data in XML | 2iu4_validation.xml.gz | 29 KB | Display | |
Data in CIF | 2iu4_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2iu4 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2iu4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 37436.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria) Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9CIW0, glucokinase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | 13 ADDITIONAL N-TERMINAL AMINOACIDS THAT OCCUR NATURALLY INCLUDED NAMELY MEFYNSTNEIPEE. THE PROTEIN ...13 ADDITIONAL | |
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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: 3.54 Å3/Da / Density % sol: 65 % |
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Crystal grow | pH: 4.5 Details: 0.1 M SODIUM ACETATE TRIHYDRATE, PH 4.5, 2 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2154 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2154 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→40 Å / Num. obs: 77167 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.39 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.17 |
Reflection shell | Resolution: 1.96→2.04 Å / Redundancy: 4.54 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.66 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.71 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 29.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→30 Å
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Refine LS restraints |
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