+Open data
-Basic information
Entry | Database: PDB / ID: 2iu6 | ||||||
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Title | REGULATION OF THE DHA OPERON OF LACTOCOCCUS LACTIS | ||||||
Components | DIHYDROXYACETONE KINASE | ||||||
Keywords | TRANSFERASE / KINASE / DIHYDROXYACETONE KINASE TRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LACTOCOCCUS LACTIS (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 | 2iu6.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iu6.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 2iu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iu6_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 2iu6_full_validation.pdf.gz | 463.6 KB | Display | |
Data in XML | 2iu6_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 2iu6_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2iu6 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2iu6 | HTTPS FTP |
-Related structure data
Related structure data | 2iu4C 2iu5C 1oi2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 3
NCS ensembles :
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-Components
#1: Protein | Mass: 37347.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria) Strain: IL1403 / Description: NESTLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CIW0, glucokinase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | 13 ADDITIONAL N-TERMINAL AMINO ACIDS THAT OCCUR NATURALLY INCLUDED NAMELY MEFYNSTNEIPEE. THE ...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: 2.97 Å3/Da / Density % sol: 58.26 % |
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Crystal grow | pH: 7 / Details: 0.15 M DL-MALIC ACID PH 7.0, 20% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS-IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 59910 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 12.38 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 10.95 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 6.88 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OI2 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.286 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
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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: 30.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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