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Yorodumi- PDB-3cr3: Structure of a transient complex between Dha-kinase subunits DhaM... -
+Open data
-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 | ||||||
Components |
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Keywords | TRANSFERASE / Transient Protein-protein complex TRANSFERASE complex PTS-DEPENDENT DIHYDROXYACETONE KINASE / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphotransferase system | ||||||
Function / homology | Function and homology information 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 | Lactococcus lactis subsp. lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Jeckelmann, J.M. / Zurbriggen, A. / Christen, S. / Baumann, U. / Erni, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cr3.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cr3.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cr3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3cr3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3cr3_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 3cr3_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/3cr3 ftp://data.pdbj.org/pub/pdb/validation_reports/cr/3cr3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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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.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: IL1403 / Gene: dhaL / Plasmid: pMS-DhaKLM / Production host: Escherichia coli (E. coli) / Strain (production host): CB-delta-KLM 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.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Gene: dhaM / Plasmid: pMS-DhaKLM / Production host: Escherichia coli (E. coli) / Strain (production host): CB-delta-KLM 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 0.97885,0.97823,0.97240 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→66.23 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.876 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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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