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Yorodumi- PDB-1gsj: Selenomethionine substituted N-acetyl-L-glutamate kinase from Esc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gsj | ||||||
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Title | Selenomethionine substituted N-acetyl-L-glutamate kinase from Escherichia coli complexed with its substrate n-acetyl-L-glutamate and its substrate analog AMPPNP | ||||||
Components | ACETYLGLUTAMATE KINASE | ||||||
Keywords | KINASE / ACETYLGLUTAMATE KINASE / SELENOMETHIONINE / CARBAMATE KINASE / AMINO ACID KINASE / ARGININE BIOSYNTHESIS / PHOSPHORYL GROUP TRANSFER / PROTEIN CRYSTALLOGRAPHY | ||||||
Function / homology | Function and homology information acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / DNA damage response / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Ramon-Maiques, S. / Marina, A. / Gil-Ortiz, F. / Fita, I. / Rubio, V. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structure of Acetylglutamate Kinase, a Key Enzyme for Arginine Biosynthesis and a Prototype for the Amino Acid Kinase Enzyme Family, During Catalysis Authors: Ramon-Maiques, S. / Marina, A. / Gil-Ortiz, F. / Fita, I. / Rubio, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gsj.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gsj.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 1gsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/1gsj ftp://data.pdbj.org/pub/pdb/validation_reports/gs/1gsj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27561.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SELENOMETHIONINE SUBSTITUTED ENZYME / Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Description: FROM NOVAGEN / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) PLYSS References: UniProt: P11445, UniProt: P0A6C8*PLUS, acetylglutamate kinase |
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#2: Chemical | ChemComp-NLG / |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Compound details | THIS ENZYME IS INVOLVED IN THE SECOND STEP OF ARGININE BIOSYNTHES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % |
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Crystal grow | pH: 4.6 Details: 27-32% PEG MONOMETHYLETHER 2000, 0.1-0.3M AMMONIUM SULFATE, 5% ETHYLENE GLYCOL, 0.1M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.94, 0.9765, 0.9770 | ||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 1999 / Details: TOROIDAL MIRROR | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.82→29.8 Å / Num. obs: 20642 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11 | ||||||||||||
Reflection shell | Resolution: 1.82→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.5 / % possible all: 97.8 | ||||||||||||
Reflection | *PLUS Num. measured all: 106899 | ||||||||||||
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→19.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2952440.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.7768 Å2 / ksol: 0.356637 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 29.88 Å / Num. reflection obs: 18562 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.216 |