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- PDB-4ald: HUMAN MUSCLE FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE COMPLEXED WITH FR... -

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Basic information

Entry
Database: PDB / ID: 4ald
TitleHUMAN MUSCLE FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE COMPLEXED WITH FRUCTOSE 1,6-BISPHOSPHATE
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE
KeywordsLYASE / LYASE (ALDEHYDE) / COMPLEX / TYPE 1 ALDOLASE / TIM BARREL
Function / homology
Function and homology information


fructose binding / sperm head / ATP biosynthetic process / binding of sperm to zona pellucida / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / Gluconeogenesis / fructose metabolic process / M band / I band ...fructose binding / sperm head / ATP biosynthetic process / binding of sperm to zona pellucida / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / Gluconeogenesis / fructose metabolic process / M band / 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 / actin filament organization / glycolytic process / actin cytoskeleton / tertiary granule lumen / Platelet degranulation / regulation of cell shape / actin binding / secretory granule lumen / protein homotetramerization / 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
1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsDalby, A.R. / Dauter, Z. / Littlechild, J.A.
Citation
Journal: Protein Sci. / Year: 1999
Title: Crystal structure of human muscle aldolase complexed with fructose 1,6-bisphosphate: mechanistic implications.
Authors: Dalby, A. / Dauter, Z. / Littlechild, J.A.
#1: 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.
#2: Journal: FEBS Lett. / Year: 1990
Title: The Crystal Structure of Human Muscle Aldolase at 3.0 A Resolution
Authors: Gamblin, S.J. / Cooper, B. / Millar, J.R. / Davies, G.J. / Littlechild, J.A. / Watson, H.C.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Molecular Architecture of Rabbit Skeletal Muscle Aldolase at 2.7-A Resolution
Authors: Sygusch, J. / Beaudry, D. / Allaire, M.
History
DepositionJul 26, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6792
Polymers39,3391
Non-polymers3401
Water00
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE
hetero molecules

A: FRUCTOSE-BISPHOSPHATE ALDOLASE
hetero molecules

A: FRUCTOSE-BISPHOSPHATE ALDOLASE
hetero molecules

A: FRUCTOSE-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,7168
Polymers157,3554
Non-polymers1,3604
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 area12860 Å2
ΔGint-50 kcal/mol
Surface area50970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.500, 96.500, 166.900
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 FRUCTOSE-BISPHOSPHATE ALDOLASE


Mass: 39338.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: LEG TISSUE / Source: (natural) Homo sapiens (human) / Organ: SKELETAL / Tissue: MUSCLE / References: UniProt: P04075, fructose-bisphosphate aldolase
#2: Sugar ChemComp-2FP / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)


Type: saccharide / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 56.9 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown
Details: Millar, J.R., (1981) Phil. Trans. R. Soc. Lond. B, 293, 209.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.95
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.8→19.56 Å / Num. obs: 11099 / % possible obs: 93.7 % / Redundancy: 4 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 31
Reflection
*PLUS
Highest resolution: 2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.8→19.56 Å / SU B: 13.1 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.65 / ESU R Free: 0.44
RfactorNum. reflection% reflectionSelection details
Rfree0.304 548 5 %RANDOM
Rwork0.202 ---
obs-10539 93.7 %-
Displacement parametersBiso mean: 17.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 20 0 2783
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0280.02
X-RAY DIFFRACTIONp_angle_d0.0780.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.1120.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.2240.3
X-RAY DIFFRACTIONp_multtor_nbd0.2820.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2010.3
X-RAY DIFFRACTIONp_planar_tor15.47
X-RAY DIFFRACTIONp_staggered_tor24.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.920
X-RAY DIFFRACTIONp_special_tor15
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor obs: 0.226 / Rfactor Rfree: 0.299 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS

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