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Yorodumi- PDB-6ofu: X-ray crystal structure of the YdjI aldolase from Escherichia coli K12 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ofu | |||||||||
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Title | X-ray crystal structure of the YdjI aldolase from Escherichia coli K12 | |||||||||
Components | YdjI aldolase | |||||||||
Keywords | LYASE / aldolase | |||||||||
Function / homology | Function and homology information tagatose-bisphosphate aldolase activity / carbohydrate metabolic process / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Dopkins, B.J. / Thoden, J.B. / Huddleston, J.P. / Narindoshvili, T. / Fose, B. / Rachel, F.M. / Holden, H.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2019 Title: Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity inEscherichia coliK12. Authors: Huddleston, J.P. / Thoden, J.B. / Dopkins, B.J. / Narindoshvili, T. / Fose, B.J. / Holden, H.M. / Raushel, F.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ofu.cif.gz | 236.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ofu.ent.gz | 186.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ofu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ofu_validation.pdf.gz | 464.7 KB | Display | wwPDB validaton report |
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Full document | 6ofu_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 6ofu_validation.xml.gz | 48.3 KB | Display | |
Data in CIF | 6ofu_validation.cif.gz | 71.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/6ofu ftp://data.pdbj.org/pub/pdb/validation_reports/of/6ofu | HTTPS FTP |
-Related structure data
Related structure data | 1gvfS 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: 31965.918 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ydjI, b1773, JW1762 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P77704 #2: Chemical | ChemComp-ZN / #3: Chemical | #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: 2.14 Å3/Da / Density % sol: 42.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10-12% PEG5000 100 mM MES 5 mM DHAP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 104686 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 7205 / Rsym value: 0.213 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1gvf Resolution: 1.75→34.74 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.981 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.099 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.881 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→34.74 Å
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Refine LS restraints |
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