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Yorodumi- PDB-1oh9: Acetylglutamate kinase from Escherichia coli complexed with MgADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oh9 | ||||||
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Title | Acetylglutamate kinase from Escherichia coli complexed with MgADP, N-acetyl-L-glutamate and the transition-state mimic AlF4- | ||||||
Components | ACETYLGLUTAMATE KINASE | ||||||
Keywords | KINASE / N-ACETYL-L-GLUTAMATE KINASE / AMINO ACID KINASE / PHOSPHORYL N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / GROUP TRANSFER / ARGININE METABOLISM | ||||||
Function / homology | Function and homology information acetylglutamate kinase / acetylglutamate kinase activity / acetyl-CoA:L-glutamate N-acetyltransferase activity / N-acetyl-gamma-glutamyl-phosphate reductase activity / arginine biosynthetic process via ornithine / glutamate metabolic process / arginine biosynthetic process / phosphorylation / DNA damage response / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Gil-Ortiz, F. / Ramon-Maiques, S. / Fita, I. / Rubio, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The Course of Phosphorus in the Reaction of N-Acetyl-L-Glutamate Kinase, Determined from the Structures of Crystalline Complexes, Including a Complex with an Alf(4)(-) Transition State Mimic Authors: Gil-Ortiz, F. / Ramon-Maiques, S. / 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 | 1oh9.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oh9.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oh9_validation.pdf.gz | 742 KB | Display | wwPDB validaton report |
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Full document | 1oh9_full_validation.pdf.gz | 744.9 KB | Display | |
Data in XML | 1oh9_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 1oh9_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1oh9 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1oh9 | HTTPS FTP |
-Related structure data
Related structure data | 1ohaC 1ohbC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27186.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Plasmid: PNAGK24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P11445, UniProt: P0A6C8*PLUS, acetylglutamate kinase |
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-Non-polymers , 5 types, 214 molecules
#2: Chemical | ChemComp-ADP / |
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#3: Chemical | ChemComp-NLG / |
#4: Chemical | ChemComp-ALF / |
#5: Chemical | ChemComp-MG / |
#6: 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: 41 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 27-29% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2K, SODIUM ACETATE 0.1M PH 4.6 AMMONIUM CITRATE 0.25-0.4 M | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 4, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8424 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→30.02 Å / Num. obs: 18025 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.91→2.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 5.3 / % possible all: 95 |
Reflection | *PLUS Highest resolution: 1.91 Å / Lowest resolution: 30.02 Å / Num. measured all: 89855 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 95 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 5.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GS5 Resolution: 1.91→30 Å / Rfactor Rfree error: 0.0078 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: ISOMORPHOUS CRYSTALS WITH 1GS5 ALLOWED A PURE RIGID-BODY APPROACH
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.5073 Å2 / ksol: 0.373379 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.91→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→2.03 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Refinement | *PLUS Num. reflection obs: 17143 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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