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Yorodumi- PDB-5zol: Crystal structure of a three sites mutantion of FSAA complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zol | ||||||
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Title | Crystal structure of a three sites mutantion of FSAA complexed with HA and product | ||||||
Components | Fructose-6-phosphate aldolase 1 | ||||||
Keywords | LYASE / Fructose-6-phosphate aldolase / donor / acceptor / mutant / flexible | ||||||
Function / homology | Function and homology information ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.172 Å | ||||||
Authors | Wu, L. / Yang, X.H. / Yu, H.W. / Zhou, J.H. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2020 Title: The engineering of decameric d-fructose-6-phosphate aldolase A by combinatorial modulation of inter- and intra-subunit interactions. Authors: Yang, X. / Wu, L. / Li, A. / Ye, L. / Zhou, J. / Yu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zol.cif.gz | 432.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zol.ent.gz | 363.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zol_validation.pdf.gz | 596.7 KB | Display | wwPDB validaton report |
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Full document | 5zol_full_validation.pdf.gz | 624.7 KB | Display | |
Data in XML | 5zol_validation.xml.gz | 88.3 KB | Display | |
Data in CIF | 5zol_validation.cif.gz | 120.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/5zol ftp://data.pdbj.org/pub/pdb/validation_reports/zo/5zol | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 26928.037 Da / Num. of mol.: 10 / Mutation: T31I/T59Q/Q195I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: fsaA, fsa, mipB, ybiZ, b0825, JW5109 / Production host: Escherichia coli (E. coli) References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases |
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-Non-polymers , 6 types, 946 molecules
#2: Chemical | ChemComp-4Y8 / #3: Chemical | ChemComp-LW2 / ( #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-LW1 / | #7: 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: 2.81 Å3/Da / Density % sol: 56.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Hepes pH7.2, 18% PEG 4000, 10% isopropyl alcohol, 0.2M ammonium sulfate, 0.01M disodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 161347 / % possible obs: 99.7 % / Redundancy: 16.3 % / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.17→2.21 Å / Redundancy: 15.8 % / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.172→22.7 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.172→22.7 Å
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Refine LS restraints |
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LS refinement shell |
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