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- PDB-3zzf: Crystal structure of the amino acid kinase domain from Saccharomy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zzf | ||||||
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Title | Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase complexed with its substrate N- acetylglutamate | ||||||
![]() | ACETYLGLUTAMATE KINASE | ||||||
![]() | TRANSFERASE / N-ACETYL-L-GLUTAMATE / ARGININE BIOSYNTHESIS | ||||||
Function / homology | ![]() Urea cycle / ornithine biosynthetic process / N-acetyl-gamma-glutamyl-phosphate reductase / acetylglutamate kinase / acetylglutamate kinase activity / acetyl-CoA:L-glutamate N-acetyltransferase activity / N-acetyl-gamma-glutamyl-phosphate reductase activity / glutamate metabolic process / arginine biosynthetic process / NADP+ binding ...Urea cycle / ornithine biosynthetic process / N-acetyl-gamma-glutamyl-phosphate reductase / acetylglutamate kinase / acetylglutamate kinase activity / acetyl-CoA:L-glutamate N-acetyltransferase activity / N-acetyl-gamma-glutamyl-phosphate reductase activity / glutamate metabolic process / arginine biosynthetic process / NADP+ binding / NAD binding / protein dimerization activity / mitochondrial matrix / phosphorylation / regulation of DNA-templated transcription / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V. | ||||||
![]() | ![]() Title: Insight on an Arginine Synthesis Metabolon from the Tetrameric Structure of Yeast Acetylglutamate Kinase Authors: De Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 471.2 KB | Display | ![]() |
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PDB format | ![]() | 391.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.8 KB | Display | ![]() |
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Full document | ![]() | 517.7 KB | Display | |
Data in XML | ![]() | 47.3 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34015.039 Da / Num. of mol.: 4 / Fragment: AMINO ACID KINASE DOMAIN, RESIDUES 58-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: SIGMA 1278B / Plasmid: PYK6-AAK / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 466 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/NLG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/NLG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-HG / #5: Chemical | ChemComp-NLG / #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE; PREVIOUS TO FREEZING, CRYSTAL WAS SOAKED IN 2 MM HGCL2 AND 25% ...Details: PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE; PREVIOUS TO FREEZING, CRYSTAL WAS SOAKED IN 2 MM HGCL2 AND 25% GLYCEROL AS CRYOPROTECTOR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.97 Å / Num. obs: 67865 / % possible obs: 100 % / Observed criterion σ(I): 1.9 / Redundancy: 15 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: STARTING MODEL WAS A LOW RESOLUTION INCOMPLETE MODEL FROM A SE-MET SUBSTITUTED CRYSTAL Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.302 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.165 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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