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- PDB-1ewe: Fructose 1,6-Bisphosphate Aldolase from Rabbit Muscle -

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Basic information

Entry
Database: PDB / ID: 1ewe
TitleFructose 1,6-Bisphosphate Aldolase from Rabbit Muscle
ComponentsFRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
KeywordsLYASE / ALDOLASE / LYASE(ALDEHYDE) / SCHIFF BASE / GLYCOLISIS / ALPHA/BETA BARREL
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / I band / M band / glycolytic process / protein homotetramerization / positive regulation of cell migration
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 speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsMaurady, A. / Sygusch, J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: A conserved glutamate residue exhibits multifunctional catalytic roles in D-fructose-1,6-bisphosphate aldolases.
Authors: Maurady, A. / Zdanov, A. / De Moissac, D. / Beaudry, D. / Sygusch, J.
History
DepositionApr 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 1,6-BISPHOSPHATE ALDOLASE
B: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
C: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
D: FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,2556
Polymers157,0634
Non-polymers1922
Water43,9032437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-59 kcal/mol
Surface area54050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)164.24, 57.41, 85.05
Angle α, β, γ (deg.)90.0, 102.65, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE


Mass: 39265.688 Da / Num. of mol.: 4 / Mutation: K107M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: SKELETAL MUSCLE / Plasmid: PPB1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHAMCR / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2437 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 7.4
Details: Ammonium sulfate, 43 percent 5mM EDTA, pH 7.4, SMALL TUBES, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %satammonium sulfate1drop
210 mg/mlprotein1drop
350 %satammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
21
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
Detector
TypeIDDetectorDate
SIEMENS HI-STAR1AREA DETECTORNov 7, 1995
SIEMENS HI-STAR2AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→28.57 Å / Num. obs: 34787
Reflection
*PLUS
Num. obs: 48198 / % possible obs: 84 % / Num. measured all: 87439 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 2.6→10 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: XPLOR parhcsdx
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2783 -random
Rwork0.166 ---
all-34046 --
obs-32063 8 %-
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11028 0 10 2437 13475
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.1494
X-RAY DIFFRACTIONx_dihedral21.37
X-RAY DIFFRACTIONx_torsion_deg1.44
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 12 Å / Num. reflection obs: 34787 / σ(F): 1 / % reflection Rfree: 8 % / Rfactor obs: 0.177 / Rfactor Rfree: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.71

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