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- PDB-1fba: THE CRYSTAL STRUCTURE OF FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM ... -

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Basic information

Entry
Database: PDB / ID: 1fba
TitleTHE CRYSTAL STRUCTURE OF FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM DROSOPHILA MELANOGASTER AT 2.5 ANGSTROMS RESOLUTION
ComponentsFRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
KeywordsLYASE(ALDEHYDE)
Function / homology
Function and homology information


glyceraldehyde-3-phosphate metabolic process / Fructose catabolism / Glycolysis / Gluconeogenesis / fructose catabolic process / fructose-1-phosphate aldolase activity / Platelet degranulation / Neutrophil degranulation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity ...glyceraldehyde-3-phosphate metabolic process / Fructose catabolism / Glycolysis / Gluconeogenesis / fructose catabolic process / fructose-1-phosphate aldolase activity / Platelet degranulation / Neutrophil degranulation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / canonical glycolysis / M band / mesoderm development / glycolytic process / gluconeogenesis / Z disc / glucose homeostasis / 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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsPiontek, K. / Hester, G. / Brenner-Holzach, O.
Citation
Journal: FEBS Lett. / Year: 1991
Title: The crystal structure of fructose-1,6-bisphosphate aldolase from Drosophila melanogaster at 2.5 A resolution.
Authors: Hester, G. / Brenner-Holzach, O. / Rossi, F.A. / Struck-Donatz, M. / Winterhalter, K.H. / Smit, J.D. / Piontek, K.
#1: Journal: Arch.Biochem.Biophys. / Year: 1988
Title: Fructose-1,6-Bisphosphate Aldolase from Drosophila Melanogaster: Primary Structure Analysis, Secondary Structure Prediction, and Comparison with Vertebrate Aldolases
Authors: Malek, A.A. / Hy, M. / Honegger, A. / Rose, K. / Brenner-Holzach, O.
History
DepositionJun 8, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
B: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
C: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
D: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)155,9574
Polymers155,9574
Non-polymers00
Water32,7151816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-45 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.600, 116.800, 151.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE 158 IS A CIS PROLINE IN ALL FOUR CHAINS.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.91626, -0.04832, -0.39767), (-0.04723, -0.99881, 0.01254), (-0.3978, 0.0073, -0.91744)14.08994, 26.70957, 64.53925
2given(-1, -0.00099, -0.00273), (-0.00036, 0.97511, -0.22173), (0.00289, -0.22173, -0.9751)3.2826, 7.69806, 68.96657
3given(-0.91435, 0.0408, 0.40286), (0.04622, -0.97789, 0.20394), (0.40227, 0.20509, 0.89225)-10.83144, 19.70642, 0.22911

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Components

#1: Protein
FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE


Mass: 38989.180 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P07764, fructose-bisphosphate aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1816 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IS DESCRIBED IN REFERENCE 1 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal grow
*PLUS
Temperature: 2-4 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop / Details: referred to J.Biol.Chem. 257.11747-11749 1987
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG60001drop
2100 mMTris-HCl1drop
31 mMEDTA1drop
41 mMbeta-mercaptoethanol1drop
50.1 mMdithioerythritol1drop
67.5 mg/mlprotein1drop
720 %PEG60001reservoir
8100 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 123654 / % possible obs: 87 % / Num. measured all: 377901 / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→8 Å / Rfactor obs: 0.179
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10980 0 0 1816 12796
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.021

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