+Open data
-Basic information
Entry | Database: PDB / ID: 1tuy | ||||||
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Title | Acetate Kinase complexed with ADP, AlF3 and acetate | ||||||
Components | Acetate kinase | ||||||
Keywords | TRANSFERASE / alpha/beta / ASKHA (acetate and sugar kinases / hsc70 / actin) superfamily / AlF3 and acetate | ||||||
Function / homology | Function and homology information acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanosarcina thermophila (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Gorrell, A. / Lawrence, S.H. / Ferry, J.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural and Kinetic Analyses of Arginine Residues in the Active Site of the Acetate Kinase from Methanosarcina thermophila. Authors: Gorrell, A. / Lawrence, S.H. / Ferry, J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tuy.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tuy.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tuy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/1tuy ftp://data.pdbj.org/pub/pdb/validation_reports/tu/1tuy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43411.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina thermophila (archaea) / Gene: ACKA, ACK / Plasmid: pET-AK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38502, acetate kinase |
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-Non-polymers , 5 types, 54 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-AF3 / | #5: Chemical | ChemComp-ACY / | #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: 2.79 Å3/Da / Density % sol: 55.86 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Tris, lithium chloride, aluminum chloride, sodium flouride, acetate, ammonium sulfate, ADP, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.073 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.073 Å / Relative weight: 1 |
Reflection | Resolution: 3→28.43 Å / Num. all: 30164 / Num. obs: 18882 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.106 |
Reflection shell | Resolution: 3→3.19 Å / Num. unique all: 2530 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→28.43 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1756850.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.5732 Å2 / ksol: 0.396248 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→28.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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