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Yorodumi- PDB-8q5a: Crystal structure of metal-dependent class II sulfofructosephosph... -
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-Basic information
Entry | Database: PDB / ID: 8q5a | ||||||
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Title | Crystal structure of metal-dependent class II sulfofructosephosphate aldolase from Hafnia paralvei HpSqiA-Zn in complex with dihydroxyacetone phosphate (DHAP) | ||||||
Components | Ketose-bisphosphate aldolase | ||||||
Keywords | LYASE / metal-dependent / aldolase / sulfoquinovose / sulfofructose phosphate | ||||||
Function / homology | Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / aldehyde-lyase activity / Aldolase-type TIM barrel / carbohydrate metabolic process / zinc ion binding / 1,3-DIHYDROXYACETONEPHOSPHATE / Ketose-bisphosphate aldolase Function and homology information | ||||||
Biological species | Hafnia paralvei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 8q5a.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q5a.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 8q5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q5a_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8q5a_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8q5a_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 8q5a_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/8q5a ftp://data.pdbj.org/pub/pdb/validation_reports/q5/8q5a | HTTPS FTP |
-Related structure data
Related structure data | 8q57C 8q58C 8q59C 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: 33588.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hafnia paralvei (bacteria) / Gene: kbaY / Plasmid: pET28a (+) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2A2MA06 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-13P / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: A crystal of the DHAP complex grew from 14 mg mL-1 enzyme in 50 mM Tris buffer pH 7.4 in a drop with 0.15 uL protein to 0.15 uL mother liquor soaked with SFP for 2 min, with the reservoir ...Details: A crystal of the DHAP complex grew from 14 mg mL-1 enzyme in 50 mM Tris buffer pH 7.4 in a drop with 0.15 uL protein to 0.15 uL mother liquor soaked with SFP for 2 min, with the reservoir solution containing 25% PEG 1,500 w/v, 0.1 M SPG (succinic acid, propionate, glycine) buffer pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→34.22 Å / Num. obs: 7522 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Χ2: 0.99 / Net I/σ(I): 17.7 / Num. measured all: 95222 |
Reflection shell | Resolution: 2.8→2.95 Å / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.439 / Num. measured all: 14614 / Num. unique obs: 1087 / CC1/2: 0.971 / Rpim(I) all: 0.123 / Rrim(I) all: 0.456 / Χ2: 0.95 / Net I/σ(I) obs: 5.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→34 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.866 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / 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: 46.956 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→34 Å
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