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Yorodumi- PDB-3zzg: Crystal structure of the amino acid kinase domain from Saccharomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zzg | ||||||
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Title | Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase without ligands | ||||||
Components | ACETYLGLUTAMATE KINASE | ||||||
Keywords | TRANSFERASE / ARGININE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information Urea cycle / ornithine biosynthetic process / N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process / NADP+ binding / NAD binding / protein dimerization activity ...Urea cycle / ornithine biosynthetic process / N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / acetylglutamate kinase / acetylglutamate kinase activity / 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 | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | de Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V. | ||||||
Citation | Journal: Plos One / Year: 2012 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zzg.cif.gz | 461.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zzg.ent.gz | 387.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzg ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzg | HTTPS FTP |
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-Related structure data
Related structure data | 3zzfSC 3zzhC 3zziC 4ab7C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#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.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: SIGMA 1278B / Plasmid: PYK6-AAK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01217, acetylglutamate kinase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48 % / 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 (NAG); PREVIOUS TO FREEZING, CRYSTAL WAS WASHED 6 HOURS IN ...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 (NAG); PREVIOUS TO FREEZING, CRYSTAL WAS WASHED 6 HOURS IN CRYSTALLIZATION BUFFER WITHOUT NAG. 25% GLYCEROL WAS USED AS CRYOPROTECTOR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→20 Å / Num. obs: 28023 / % possible obs: 99.8 % / Observed criterion σ(I): 2.1 / Redundancy: 6.4 % / Biso Wilson estimate: 79.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZZF Resolution: 2.95→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / SU B: 40.766 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.447 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→20 Å
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Refine LS restraints |
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