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Yorodumi- PDB-1xdl: Structure of human aldolase B associated with hereditary fructose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xdl | ||||||
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Title | Structure of human aldolase B associated with hereditary fructose intolerance (A149P), at 277K | ||||||
Components | Fructose-bisphosphate aldolase B | ||||||
Keywords | LYASE / ALPHA/BETA BARREL | ||||||
Function / homology | Function and homology information fructose-1-phosphate aldolase activity / Hereditary fructose intolerance / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / fructose binding / vacuolar proton-transporting V-type ATPase complex assembly / Fructose catabolism / NADH oxidation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / Gluconeogenesis ...fructose-1-phosphate aldolase activity / Hereditary fructose intolerance / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / fructose binding / vacuolar proton-transporting V-type ATPase complex assembly / Fructose catabolism / NADH oxidation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / Gluconeogenesis / positive regulation of ATP-dependent activity / fructose metabolic process / negative regulation of pentose-phosphate shunt / fructose 1,6-bisphosphate metabolic process / Glycolysis / microtubule organizing center / centriolar satellite / cytoskeletal protein binding / gluconeogenesis / glycolytic process / ATPase binding / molecular adaptor activity / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Malay, A.D. / Allen, K.N. / Tolan, D.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structure of the thermolabile mutant aldolase B, A149P: molecular basis of hereditary fructose intolerance. Authors: Malay, A.D. / Allen, K.N. / Tolan, D.R. #1: Journal: Arch.Biochem.Biophys. / Year: 2002 Title: The temperature dependence of activity and structure for the most prevalent mutant aldolase B associated with hereditary fructose intolerance Authors: Malay, A.D. / Procious, S.L. / Tolan, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xdl.cif.gz | 449.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xdl.ent.gz | 370.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xdl_validation.pdf.gz | 529.3 KB | Display | wwPDB validaton report |
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Full document | 1xdl_full_validation.pdf.gz | 693.7 KB | Display | |
Data in XML | 1xdl_validation.xml.gz | 104.1 KB | Display | |
Data in CIF | 1xdl_validation.cif.gz | 139.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/1xdl ftp://data.pdbj.org/pub/pdb/validation_reports/xd/1xdl | HTTPS FTP |
-Related structure data
Related structure data | 1xdmC 1qo5S 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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Unit cell |
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Details | The biological unit of AP-aldolase is a dimer, corresponding to monomer pairs AB, CD, WX, and YZ. The wild-type enzyme is tetrameric. |
-Components
#1: Protein | Mass: 39558.938 Da / Num. of mol.: 8 / Mutation: A149P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDOB, ALDB / Organ: liver / Plasmid: pGEX-AP / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P05062, fructose-bisphosphate aldolase #2: Chemical | ChemComp-SO4 / #3: 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: 3.4 Å3/Da / Density % sol: 63.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: ammonium sulfate, 1,8-diaminooctane, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2001 / Details: Rh mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. all: 96334 / Num. obs: 91423 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rsym value: 0.061 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 8580 / Rsym value: 0.283 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QO5 Resolution: 3→20.15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 435505.96 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: used ncs restraints between monomers
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.23773 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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