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- PDB-2ald: HUMAN MUSCLE ALDOLASE -

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Basic information

Entry
Database: PDB / ID: 2ald
TitleHUMAN MUSCLE ALDOLASE
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE
KeywordsLYASE / LYASE (ALDEHYDE) / TYPE I ALDOLASE
Function / homology
Function and homology information


fructose binding / sperm head / ATP biosynthetic process / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / binding of sperm to zona pellucida / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / Gluconeogenesis / M band ...fructose binding / sperm head / ATP biosynthetic process / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / binding of sperm to zona pellucida / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / Gluconeogenesis / M band / I band / Glycolysis / muscle cell cellular homeostasis / striated muscle contraction / cytoskeletal protein binding / tubulin binding / platelet alpha granule lumen / actin filament organization / glycolytic process / actin cytoskeleton / Platelet degranulation / tertiary granule lumen / actin binding / regulation of cell shape / protein homotetramerization / secretory granule lumen / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDalby, A.R. / 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: FEBS Lett. / Year: 1990
Title: Erratum. 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.
#4: 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
DepositionOct 21, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)39,3391
Polymers39,3391
Non-polymers00
Water2,576143
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE

A: FRUCTOSE-BISPHOSPHATE ALDOLASE

A: FRUCTOSE-BISPHOSPHATE ALDOLASE

A: FRUCTOSE-BISPHOSPHATE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)157,3554
Polymers157,3554
Non-polymers00
Water724
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 area10710 Å2
ΔGint-38 kcal/mol
Surface area50390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.500, 96.500, 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 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: SKELETALSkeleton / Tissue: MUSCLESkeletal muscle / References: UniProt: P04075, fructose-bisphosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55 %
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
DetectorDetector: FILM
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→19.68 Å / Num. obs: 21561 / % possible obs: 78.7 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.06
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / SU B: 4.78 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 -5 %RANDOM
Rwork0.172 ---
obs-21561 78.7 %-
Displacement parametersBiso mean: 29.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 0 143 2906
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0420.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.088
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.1613
X-RAY DIFFRACTIONp_mcangle_it4.1285
X-RAY DIFFRACTIONp_scbond_it7.4456
X-RAY DIFFRACTIONp_scangle_it9.3998
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.3
X-RAY DIFFRACTIONp_multtor_nbd0.2990.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1090.3
X-RAY DIFFRACTIONp_planar_tor14.47
X-RAY DIFFRACTIONp_staggered_tor21.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.172 / Rfactor obs: 0.162 / Highest resolution: 2.1 Å / Lowest resolution: 19.68 Å / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS

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