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Yorodumi- PDB-6xio: ADP-dependent kinase complex with fructose-6-phosphate and ADPbetaS -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xio | ||||||||||||
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Title | ADP-dependent kinase complex with fructose-6-phosphate and ADPbetaS | ||||||||||||
Components | ADP-dependent phosphofructokinase | ||||||||||||
Keywords | TRANSFERASE / ancestral protein reconstruction / ADP-dependent sugar kinases family / glucokinase / phosphofructokinase / enzyme evolution | ||||||||||||
Function / homology | Chem-AT4 / 6-O-phosphono-beta-D-fructofuranose Function and homology information | ||||||||||||
Biological species | Methanosarcinales archaeon (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | ||||||||||||
Authors | Munoz, S. / Gonzalez-Ordenes, F. / Fuentes, N. / Maturana, P. / Herrera-Morande, A. / Villalobos, P. / Castro-Fernandez, V. | ||||||||||||
Funding support | Chile, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structure of an ancestral ADP-dependent kinase with fructose-6P reveals key residues for binding, catalysis, and ligand-induced conformational changes. Authors: Munoz, S.M. / Castro-Fernandez, V. / Guixe, V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xio.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xio.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 6xio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/6xio ftp://data.pdbj.org/pub/pdb/validation_reports/xi/6xio | HTTPS FTP |
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-Related structure data
Related structure data | 6c8zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57768.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcinales archaeon (archaea) / Production host: Escherichia coli (E. coli) / References: ADP-specific phosphofructokinase |
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#2: Chemical | ChemComp-AT4 / |
#3: Sugar | ChemComp-F6P / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: Protein Condition: F6P 6 mM, mM ADPbs 2.4 mM, MgCl2 7.4 mM , HEPES 25 mM pH 7.8, NaCl 200 mM and 2-mercaptoethanol 1 mM; Reservoir Condition: PEG 20,000 8.4% w/V, MgCl2 0.2M, Sodium citrate 0.1M pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45867 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 6, 2017 |
Radiation | Monochromator: Double Crystal Monochromator - Water-cooled Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45867 Å / Relative weight: 1 |
Reflection | Resolution: 3.12→44.85 Å / Num. obs: 10902 / % possible obs: 98.3 % / Redundancy: 12.4 % / Biso Wilson estimate: 88.84 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1507 / Rpim(I) all: 0.04486 / Rrim(I) all: 0.1574 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 3.12→3.23 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 3.02 / Num. unique obs: 1053 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.2532 / Rrim(I) all: 0.879 / % possible all: 99.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6C8Z Resolution: 3.12→44.85 Å / SU ML: 0.4712 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2544 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.77 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.12→44.85 Å
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Refine LS restraints |
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LS refinement shell |
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