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Yorodumi- PDB-1gs5: N-acetyl-L-glutamate kinase from Escherichia coli complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gs5 | ||||||
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Title | N-acetyl-L-glutamate kinase from Escherichia coli complexed with its substrate N-acetylglutamate and its substrate analog AMPPNP | ||||||
Components | ACETYLGLUTAMATE KINASE | ||||||
Keywords | TRANSFERASE / CARBAMATE KINASE / AMINO ACID KINASE / ARGININE BIOSYNTHESIS / PHOSPHORYL GROUP TRANSFER | ||||||
Function / homology | Function and homology information acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / L-arginine biosynthetic process / DNA damage response / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 1gs5.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gs5.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gs5_validation.pdf.gz | 739.7 KB | Display | wwPDB validaton report |
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Full document | 1gs5_full_validation.pdf.gz | 751.3 KB | Display | |
Data in XML | 1gs5_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1gs5_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/1gs5 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/1gs5 | HTTPS FTP |
-Related structure data
Related structure data | 1gsjSC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27186.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Description: NOVAGEN / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) 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 / |
-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: ESRF / Beamline: ID14-1 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→53.71 Å / Num. obs: 37460 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.042 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.349 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 37500 / Num. measured all: 196777 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.349 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GSJ Resolution: 1.5→50 Å / SU B: 1.60017 / SU ML: 0.06101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.09127 / Details: NONE
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 53.71 Å / Num. reflection Rfree: 1861 / Rfactor obs: 0.2088 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.661 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.241 / Num. reflection Rwork: 472 / Total num. of bins used: 10 / Rfactor obs: 0.241 |