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- PDB-3cr3: Structure of a transient complex between Dha-kinase subunits DhaM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cr3 | ||||||
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Title | Structure of a transient complex between Dha-kinase subunits DhaM and DhaL from Lactococcus lactis | ||||||
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![]() | TRANSFERASE / Transient Protein-protein complex TRANSFERASE complex PTS-DEPENDENT DIHYDROXYACETONE KINASE / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphotransferase system | ||||||
Function / homology | ![]() phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / glycerone kinase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycerol catabolic process / phosphorylation / magnesium ion binding / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeckelmann, J.M. / Zurbriggen, A. / Christen, S. / Baumann, U. / Erni, B. | ||||||
![]() | ![]() Title: X-ray Structures of the Three Lactococcus lactis Dihydroxyacetone Kinase Subunits and of a Transient Intersubunit Complex. Authors: Zurbriggen, A. / Jeckelmann, J.M. / Christen, S. / Bieniossek, C. / Baumann, U. / Erni, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 108.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 5
NCS ensembles :
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Components
#1: Protein | Mass: 20909.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: lacI(q), oriR ColE1, bla Source: (gene. exp.) ![]() Strain: IL1403 / Gene: dhaL / Plasmid: pMS-DhaKLM / Production host: ![]() ![]() References: UniProt: Q9CIV7, Transferases; Transferring phosphorus-containing groups #2: Protein | Mass: 13360.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dhaM / Plasmid: pMS-DhaKLM / Production host: ![]() ![]() References: UniProt: Q9CIV6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris/HCl, 0.2 M LiSO4, 36 % PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→147.442 Å / Num. all: 37982 / Num. obs: 37982 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 22.2 | ||||||||||||
Reflection shell | Resolution: 2.1→2.21 Å / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 8.1 / Num. unique all: 5440 / Rsym value: 0.214 / % possible all: 24.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→66.23 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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