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Yorodumi- PDB-5uck: Class II fructose-1,6-bisphosphate aldolase of Helicobacter pylor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uck | ||||||
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Title | Class II fructose-1,6-bisphosphate aldolase of Helicobacter pylori with cleavage products | ||||||
Components | Fructose-bisphosphate aldolase | ||||||
Keywords | LYASE / Glycolysis / Metalloenzyme | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å | ||||||
Authors | Jacques, B. / Sygusch, J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases. Authors: Jacques, B. / Coincon, M. / Sygusch, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uck.cif.gz | 340.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uck.ent.gz | 282.7 KB | Display | PDB format |
PDBx/mmJSON format | 5uck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/5uck ftp://data.pdbj.org/pub/pdb/validation_reports/uc/5uck | HTTPS FTP |
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-Related structure data
Related structure data | 5ucnC 5ucpC 5ucsC 5uczC 5ud0C 5ud1C 5ud2C 5ud3C 5ud4C 5vjdC 5vjeC 5vjfC 3c4uS C: citing same article (ref.) 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33800.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: fba, HP_0176 / Production host: Escherichia coli (E. coli) / References: UniProt: P56109, fructose-bisphosphate aldolase |
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-Non-polymers , 5 types, 391 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | #6: 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: 2.21 Å3/Da / Density % sol: 44.32 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 1000, PEG 8000, Calcium acetate, Tris-Acetic acid buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.782→45.19 Å / Num. obs: 51940 / % possible obs: 85.29 % / Redundancy: 1.9 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0586 / Net I/σ(I): 9.02 |
Reflection shell | Resolution: 1.782→1.846 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4454 / Mean I/σ(I) obs: 1.26 / CC1/2: 0.783 / % possible all: 60.81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C4U Resolution: 1.782→45.19 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 29.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.782→45.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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