+Open data
-Basic information
Entry | Database: PDB / ID: 2buf | |||||||||
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Title | Arginine Feed-Back Inhibitable Acetylglutamate Kinase | |||||||||
Components | ACETYLGLUTAMATE KINASE | |||||||||
Keywords | TRANSFERASE / ACETYGLUTAMATE KINASE / ACETYLGLUTAMATE / ADP / ARGININE BIOSYNTHESIS / FEED-BACK INHIBITION / HEXAMER / ARGININE INHIBITION / ALLOSTERIC MECHANISM / FEEDBACK CONTROL / AMINO ACID KINASE FAMILY | |||||||||
Function / homology | Function and homology information acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / arginine binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Ramon-Maiques, S. / Fernandez-Murga, M.L. / Vagin, A. / Fita, I. / Rubio, V. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Bases of Feed-Back Control of Arginine Biosynthesis, Revealed by the Structure of Two Hexameric N-Acetylglutamate Kinases, from Thermotoga Maritima and Pseudomonas Aeruginosa Authors: Ramon-Maiques, S. / Fernandez-Murga, M.L. / Gil-Ortiz, F. / Vagin, A. / Fita, I. / Rubio, V. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Towards Structural Understanding of Feedback Control of Arginine Biosynthesis: Cloning and Expression of the Gene for the Arginine-Inhibited N-Acetyl-L-Glutamate Kinase from Pseudomonas ...Title: Towards Structural Understanding of Feedback Control of Arginine Biosynthesis: Cloning and Expression of the Gene for the Arginine-Inhibited N-Acetyl-L-Glutamate Kinase from Pseudomonas Aeruginosa, Purification and Crystallization of the Recombinant Enzyme and Preliminary X-Ray Studies Authors: Fernandez-Murga, M.L. / Ramon-Maiques, S. / Gil-Ortiz, F. / Fita, I. / Rubio, V. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2buf.cif.gz | 640.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2buf.ent.gz | 526 KB | Display | PDB format |
PDBx/mmJSON format | 2buf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2buf_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 2buf_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 2buf_validation.xml.gz | 154.4 KB | Display | |
Data in CIF | 2buf_validation.cif.gz | 194.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/2buf ftp://data.pdbj.org/pub/pdb/validation_reports/bu/2buf | HTTPS FTP |
-Related structure data
Related structure data | 2btyC 1gs5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31754.838 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PNAGK-PA25 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HTN2, acetylglutamate kinase #2: Chemical | ChemComp-NLG / #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CL / |
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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: 2.89 Å3/Da / Density % sol: 57.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: CRYSTALS WERE OBTAINED AT 277 K IN ABOUT TWO WEEKS USING THE HANGING DROP TECHNIQUE AND UTILIZING A 10 MG/ML. PROTEIN SOLUTION CONTAINING 20 MM HEPES PH 7.5, 1 MM DITHIOERYTHRITOL, 10% ...Details: CRYSTALS WERE OBTAINED AT 277 K IN ABOUT TWO WEEKS USING THE HANGING DROP TECHNIQUE AND UTILIZING A 10 MG/ML. PROTEIN SOLUTION CONTAINING 20 MM HEPES PH 7.5, 1 MM DITHIOERYTHRITOL, 10% GLYCEROL, 30 MM MAGNESIUM CHLORIDE, 20 MM N-ACETYL-L-GLUTAMATE, 10 MM ADP AND 0.02% SODIUM AZIDE, AND A RESERVOIR SOLUTION WITH 0.1 M SODIUM CACODYLATE PH 6.5, 150-170 MM MAGNESIUM ACETATE AND POLYETHYLENE GLYCOL 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.973948 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973948 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→69 Å / Num. obs: 86766 / % possible obs: 96.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 86.056 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.95→3.1 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GS5 Resolution: 2.95→18 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 88.333 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→18 Å
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Refine LS restraints |
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Xplor file |
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