+Open data
-Basic information
Entry | Database: PDB / ID: 6xmm | ||||||
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Title | Human aldolase A I98S | ||||||
Components | Fructose-bisphosphate aldolase A | ||||||
Keywords | LYASE / rheostat / allosterism | ||||||
Function / homology | Function and homology information fructose binding / sperm head / ATP biosynthetic process / fructose-bisphosphate aldolase / binding of sperm to zona pellucida / fructose-bisphosphate aldolase activity / Gluconeogenesis / M band / fructose metabolic process / I band ...fructose binding / sperm head / ATP biosynthetic process / fructose-bisphosphate aldolase / binding of sperm to zona pellucida / fructose-bisphosphate aldolase activity / Gluconeogenesis / M band / fructose metabolic process / I band / fructose 1,6-bisphosphate metabolic process / Glycolysis / muscle cell cellular homeostasis / striated muscle contraction / cytoskeletal protein binding / tubulin binding / platelet alpha granule lumen / glycolytic process / actin filament organization / actin cytoskeleton / tertiary granule lumen / Platelet degranulation / actin binding / regulation of cell shape / protein homotetramerization / secretory granule lumen / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Meneely, K.M. / Brewer, K. / Lamb, A.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Substitutions at a rheostat position in human aldolase A cause a shift in the conformational population. Authors: Fenton, K.D. / Meneely, K.M. / Wu, T. / Martin, T.A. / Swint-Kruse, L. / Fenton, A.W. / Lamb, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xmm.cif.gz | 284.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xmm.ent.gz | 217.4 KB | Display | PDB format |
PDBx/mmJSON format | 6xmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xmm_validation.pdf.gz | 471.6 KB | Display | wwPDB validaton report |
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Full document | 6xmm_full_validation.pdf.gz | 483.4 KB | Display | |
Data in XML | 6xmm_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 6xmm_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/6xmm ftp://data.pdbj.org/pub/pdb/validation_reports/xm/6xmm | HTTPS FTP |
-Related structure data
Related structure data | 6xmhC 6xmlC 6xmoC 1aldS S: Starting model for refinement C: citing same article (ref.) |
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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: 39443.898 Da / Num. of mol.: 2 / Mutation: I98S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDOA, ALDA / Production host: Escherichia coli (E. coli) / References: UniProt: P04075, fructose-bisphosphate aldolase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 4.04 Å3/Da / Density % sol: 69.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10% (w/v) PEG 8000, 15% (v/v) glycerol, 0.04 M potassium phosphate, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2019 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→140.5 Å / Num. obs: 39448 / % possible obs: 88.4 % / Redundancy: 18.2 % / Biso Wilson estimate: 42.83 Å2 / Rpim(I) all: 0.068 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.11→2.42 Å / Num. unique obs: 1972 / Rpim(I) all: 0.738 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ALD Resolution: 2.11→46.06 Å / SU ML: 0.2846 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.6829 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→46.06 Å
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Refine LS restraints |
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LS refinement shell |
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