|Entry||Database: PDB / ID: 2ap9|
|Title||Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551|
|Keywords||SIGNALING PROTEIN / TRANSFERASE / Structural Genomics / Protein Structure Initiative / NYSGXRC / T1702 / acetylglutamate kinase / PSI / New York SGX Research Center for Structural Genomics|
|Function / homology|
Function and homology information
acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / cell wall / arginine binding / peptidoglycan-based cell wall / phosphorylation / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Acetylglutamate kinase / Acetylglutamate kinase
Similarity search - Component
|Biological species||Mycobacterium tuberculosis (unknown)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å|
|Authors||Rajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)|
|Citation||Journal: To be Published|
Title: Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551
Authors: Rajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D.
|Structure viewer||Molecule: |
Downloads & links
A: acetylglutamate kinase
B: acetylglutamate kinase
C: acetylglutamate kinase
D: acetylglutamate kinase
E: acetylglutamate kinase
F: acetylglutamate kinase
|Details||Polypeptide chain A, B, C, D, E and F together form a biological assembly|
Mass: 31963.615 Da / Num. of mol.: 6 / Fragment: acetylglutamate kinase / Mutation: MSE/MET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (unknown) / Strain: CDC1551 / Gene: argB, Rv1654, MT1692 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3
References: UniProt: P0A4Y6, UniProt: P9WQ01*PLUS, acetylglutamate kinase
|#2: Chemical||#3: Chemical|| ChemComp-NI / ||#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.73 Å3/Da / Density % sol: 54.56 %|
|Crystal grow||Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 |
Details: 3% PEG 6000, 0.1M Tris pH 8.5, 0.1M Potassium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.975 Å|
|Detector||Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2005|
Details: Vertical focussing mirror down stream of monochromator
|Radiation||Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.975 Å / Relative weight: 1|
|Reflection||Resolution: 2.8→50 Å / Num. all: 94360 / Num. obs: 94360 / % possible obs: 94 % / Observed criterion σ(I): -1 / Redundancy: 3.17 % / Biso Wilson estimate: 14.5 Å2 / Rsym value: 0.083 / Net I/σ(I): 14.61|
|Reflection shell||Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.03 / Num. unique all: 6358 / Rsym value: 0.497 / % possible all: 63.5|
|Refinement||Method to determine structure: SAD|
Starting model: Model built based on the experimental electron density map
Resolution: 2.8→48.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 178264.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Certain regions of the model do not have well defined electron density. These are residues 143-152 and 222-231. Two solvent peaks have been refined as Magnesium ions, and one solvent peak ...Details: Certain regions of the model do not have well defined electron density. These are residues 143-152 and 222-231. Two solvent peaks have been refined as Magnesium ions, and one solvent peak has be refined as a Nickle ion (as it is bound to His6 rag).
|Solvent computation||Solvent model: FLAT MODEL / Bsol: 31.491 Å2 / ksol: 0.300298 e/Å3|
|Displacement parameters||Biso mean: 81.5 Å2|
|Refinement step||Cycle: LAST / Resolution: 2.8→48.8 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6 |
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