+Open data
-Basic information
Entry | Database: PDB / ID: 6xmh | ||||||
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Title | Human aldolase A wild type | ||||||
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: 1.95 Å | ||||||
Authors | Meneely, K.M. / 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 | 6xmh.cif.gz | 289.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xmh.ent.gz | 220.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xmh_validation.pdf.gz | 471.6 KB | Display | wwPDB validaton report |
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Full document | 6xmh_full_validation.pdf.gz | 480.3 KB | Display | |
Data in XML | 6xmh_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 6xmh_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/6xmh ftp://data.pdbj.org/pub/pdb/validation_reports/xm/6xmh | HTTPS FTP |
-Related structure data
Related structure data | 6xmlC 6xmmC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 39469.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDOA, ALDA / Plasmid: pET-15b / 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: 4.03 Å3/Da |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.75 Details: 10% (w/v) PEG 8,000, 18% (v/v) glycerol, 0.04 M potassium phosphate, pH 5.75 |
-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: 1.95→140.2 Å / Num. obs: 549062 / % possible obs: 93.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 34.86 Å2 / Rpim(I) all: 0.046 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.95→2.2 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2830 / Rpim(I) all: 0.356 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ALD Resolution: 1.95→40.85 Å / SU ML: 0.2805 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.4293 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: 39.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→40.85 Å
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Refine LS restraints |
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LS refinement shell |
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