[English] 日本語
Yorodumi- PDB-3zzh: Crystal structure of the amino acid kinase domain from Saccharomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zzh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase in complex with its feed- back inhibitor L-arginine | ||||||
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: 2.1 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 |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zzh.cif.gz | 471.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zzh.ent.gz | 390.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzh ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzh | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zzfSC 3zzgC 3zziC 4ab7C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-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.) 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 |
---|
-Non-polymers , 7 types, 556 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-NLG / #6: Chemical | ChemComp-ARG / | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE |
---|---|
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); 24 HOURS BEFORE FREEZING ARGININE 0.2 M WAS ADDED TO ...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); 24 HOURS BEFORE FREEZING ARGININE 0.2 M WAS ADDED TO CRYSTALLIZATION DROP. 20% GLYCEROL WAS USED AS CRYOPROTECTOR |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9786 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 77012 / % possible obs: 99.6 % / Observed criterion σ(I): 1.9 / Redundancy: 4.8 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZZF Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.639 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 22.225 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|