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Yorodumi- PDB-5k27: Crystal structure of ancestral protein ancMT of ADP-dependent sug... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k27 | ||||||
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Title | Crystal structure of ancestral protein ancMT of ADP-dependent sugar kinases family. | ||||||
Components | ancMT | ||||||
Keywords | TRANSFERASE / ancestral protein reconstruction / ADP-dependent sugar kinases family / glucokinase / phosphofructokinase / bifuncional enzymes / enzyme evolution | ||||||
Function / homology | Adenosine kinase, small domain - #20 / Adenosine kinase, small domain / Ribokinase / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE MONOPHOSPHATE / IODIDE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Castro-Fernandez, V. / Herrera-Morande, A. / Zamora, R. / Merino, F. / Pereira, H.M. / Brandao-Neto, J. / Garratt, R. / Guixe, V. | ||||||
Funding support | Chile, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases. Authors: Castro-Fernandez, V. / Herrera-Morande, A. / Zamora, R. / Merino, F. / Gonzalez-Ordenes, F. / Padilla-Salinas, F. / Pereira, H.M. / Brandao-Neto, J. / Garratt, R.C. / Guixe, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k27.cif.gz | 187.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k27.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 5k27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k27_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5k27_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5k27_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 5k27_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/5k27 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/5k27 | HTTPS FTP |
-Related structure data
Related structure data | 5kkgC 1u2xS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54313.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28a / Details (production host): TEV clivage site / Production host: Escherichia coli (E. coli) References: ADP-specific phosphofructokinase, ADP-specific glucose/glucosamine kinase #2: Chemical | #3: Chemical | ChemComp-IOD / #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: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 18 % (w/v) PEG 3350, 0.2 M NaI Protein 8 mg/mL, 20 mM F6P, 30 mM MgCl2, 25 mM HEPES pH 7.8, 20 mM AMP. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 26, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.58→53.42 Å / Num. obs: 33041 / % possible obs: 99.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 59.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.8 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U2X Resolution: 2.58→53.42 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.71 Å2 / Biso mean: 64.7365 Å2 / Biso min: 26.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.58→53.42 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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