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Yorodumi- PDB-2x2w: Acetylglutamate kinase from Escherichia coli bound to N-acetyl-L-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x2w | ||||||
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Title | Acetylglutamate kinase from Escherichia coli bound to N-acetyl-L-glutamyl-5-phosphate | ||||||
Components | ACETYLGLUTAMATE KINASE | ||||||
Keywords | TRANSFERASE / ARGININE BIOSYNTHESIS / ATP-BINDING / NUCLEOTIDE-BINDING / AMINO-ACID BIOSYNTHESIS / AMINO ACID KINASE FAMILY | ||||||
Function / homology | Function and homology information L-glutamate N-acetyltransferase activity / N-acetyl-gamma-glutamyl-phosphate reductase activity / acetylglutamate kinase / acetylglutamate kinase activity / glutamate metabolic process / arginine biosynthetic process via ornithine / arginine biosynthetic process / phosphorylation / DNA damage response / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gil-Ortiz, F. / Rubio, V. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2010 Title: Two crystal structures of Escherichia coli N-acetyl-L-glutamate kinase demonstrate the cycling between open and closed conformations. Authors: Gil-Ortiz, F. / Ramon-Maiques, S. / Fernandez-Murga, M.L. / 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 | 2x2w.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x2w.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 2x2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x2w_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2x2w_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2x2w_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 2x2w_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/2x2w ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x2w | HTTPS FTP |
-Related structure data
Related structure data | 2wxbSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
NCS oper: (Code: given Matrix: (0.236, 0.8912, 0.3873), Vector: |
-Components
#1: Protein | Mass: 27186.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Plasmid: PET15-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A6C8, UniProt: A0A140NEG9*PLUS, acetylglutamate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30-35 % PEG MONOMETHYL ETHER 5K, 0.1 M MES PH 6.5, 0.1-0.2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.24 Å / Num. obs: 35550 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rsym value: 0.071 / Net I/σ(I): 44 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.406 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WXB Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.35 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.156 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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