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Yorodumi- PDB-8q59: Crystal structure of metal-dependent class II sulfofructose phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q59 | ||||||
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Title | Crystal structure of metal-dependent class II sulfofructose phosphate aldolase from Yersinia aldovae in complex with sulfofructose phosphate (YaSqiA-Zn-SFP) | ||||||
Components | Tagatose-1,6-bisphosphate aldolase kbaY | ||||||
Keywords | LYASE / metal-dependent / aldolase / sulfoquinovose / sulfofructose phosphate | ||||||
Function / homology | Function and homology information tagatose-bisphosphate aldolase / tagatose-bisphosphate aldolase activity / carbohydrate metabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Yersinia aldovae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sharma, M. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Defining the molecular architecture, metal dependence, and distribution of metal-dependent class II sulfofructose-1-phosphate aldolases. Authors: Sharma, M. / Kaur, A. / Madiedo Soler, N. / Lingford, J.P. / Epa, R. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q59.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q59.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 8q59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q59_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 8q59_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 8q59_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 8q59_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/8q59 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/8q59 | HTTPS FTP |
-Related structure data
Related structure data | 8q57C 8q58C 8q5aC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 33626.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia aldovae (bacteria) / Gene: kbaY / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T9TPS2 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.18 Å3/Da / Density % sol: 61.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: enzyme in 50 mM NaPi buffer pH 7.4 soaked with SFP for 30 seconds in a drop with 0.1 uL protein- 0.2 uL mother liquor, with the reservoir solution containing 1.5 M Ammonium sulfate, 0.1 M ...Details: enzyme in 50 mM NaPi buffer pH 7.4 soaked with SFP for 30 seconds in a drop with 0.1 uL protein- 0.2 uL mother liquor, with the reservoir solution containing 1.5 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 1% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.12 Å / Num. obs: 57013 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Χ2: 0.99 / Net I/σ(I): 11.6 / Num. measured all: 400155 |
Reflection shell | Resolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.772 / Num. measured all: 29852 / Num. unique obs: 4182 / CC1/2: 0.821 / Rpim(I) all: 0.309 / Rrim(I) all: 0.832 / Χ2: 0.99 / Net I/σ(I) obs: 2.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.43 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.124 / 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: 34.482 Å2
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Refinement step | Cycle: 1 / Resolution: 2→48 Å
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