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- PDB-1ald: ACTIVITY AND SPECIFICITY OF HUMAN ALDOLASES -

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Basic information

Entry
Database: PDB / ID: 1ald
TitleACTIVITY AND SPECIFICITY OF HUMAN ALDOLASES
ComponentsALDOLASE A
KeywordsLYASE (ALDEHYDE)
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
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWatson, H.C.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Activity and specificity of human aldolases.
Authors: Gamblin, S.J. / Davies, G.J. / Grimes, J.M. / Jackson, R.M. / Littlechild, J.A. / Watson, H.C.
#1: Journal: FEBS Lett. / Year: 1990
Title: The Crystal Structure of Human Muscle Aldolase at 3.0 Angstroms Resolution
Authors: Gamblin, S.J. / Cooper, B. / Millar, J.R. / Davies, G.J. / Littlechild, J.A. / Watson, H.C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Molecular Architecture of Rabbit Skeletal Muscle Aldolase at 2.7-Angstroms Resolution
Authors: Sygusch, J. / Beaudry, D. / Allaire, M.
#3: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: The Low-Resolution Structure of Human Muscle Aldolase
Authors: Millar, J.R. / Shaw, P.J. / Stammers, D.K. / Watson, H.C.
History
DepositionMay 5, 1991Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 7, 2021Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALDOLASE A


Theoretical massNumber of molelcules
Total (without water)39,3391
Polymers39,3391
Non-polymers00
Water00
1
A: ALDOLASE A

A: ALDOLASE A

A: ALDOLASE A

A: ALDOLASE A


Theoretical massNumber of molelcules
Total (without water)157,3554
Polymers157,3554
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
crystal symmetry operation12_565x,x-y+1,-z+2/31
Buried area10470 Å2
ΔGint-32 kcal/mol
Surface area49310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.340, 96.340, 167.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein ALDOLASE A


Mass: 39338.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P04075, fructose-bisphosphate aldolase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal grow
*PLUS
pH: 7.3 / Method: other
Details: referred to 'Eagles, P. A.', (1969) J. Mol. Biol., 45, 533-544
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
20.1 Mtriethanolamine-hydrochloride11
35 mMEDTA11
444-49 %satammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. all: 23815 / Num. obs: 21427 / Observed criterion σ(I): 3

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementHighest resolution: 2 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.22 --
all-23815 -
obs-21427 95 %
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 0 0 2763
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.22 / Lowest resolution: 3 Å / Num. reflection obs: 21427
Solvent computation
*PLUS
Displacement parameters
*PLUS

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