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- PDB-2isw: Structure of Giardia fructose-1,6-biphosphate aldolase in complex... -

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Basic information

Database: PDB / ID: 2isw
TitleStructure of Giardia fructose-1,6-biphosphate aldolase in complex with phosphoglycolohydroxamate
ComponentsPutative fructose-1,6-bisphosphate aldolase
KeywordsLYASE / Class II fructose-1 / 6-bisphosphate aldolase / glycolytic pathway / Giardia lamblia / drug target
Function / homology
Function and homology information

fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHOGLYCOLOHYDROXAMIC ACID / Putative fructose-1,6-bisphosphate aldolase
Similarity search - Component
Biological speciesGiardia intestinalis (unknown)
AuthorsGalkin, A. / Herzberg, O.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Characterization, kinetics, and crystal structures of fructose-1,6-bisphosphate aldolase from the human parasite, Giardia lamblia.
Authors: Galkin, A. / Kulakova, L. / Melamud, E. / Li, L. / Wu, C. / Mariano, P. / Dunaway-Mariano, D. / Nash, T.E. / Herzberg, O.
DepositionOct 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

Structure visualization

Structure viewerMolecule:

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Deposited unit
A: Putative fructose-1,6-bisphosphate aldolase
B: Putative fructose-1,6-bisphosphate aldolase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)70,8244

  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-69 kcal/mol
Surface area22740 Å2
Unit cell
Length a, b, c (Å)90.020, 90.050, 166.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer generated from the molecules A and B in the asymmetric unit


#1: Protein Putative fructose-1,6-bisphosphate aldolase

Mass: 35293.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (unknown) / Strain: WB / Gene: ald / Plasmid: pET100/FBPAn / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: O97447, fructose-bisphosphate aldolase
#2: Chemical ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 18-23% Polyethylglycol monomethyl ether 2000, 0.1 M Tris-HCl, 0.2 M MgCl2, 20 mM PGH, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 68175 / Num. obs: 56981 / % possible obs: 83.6 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.492 / % possible all: 75.2


DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JVF

PDB Unreleased entry

Resolution: 1.75→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2877 -RANDOM
Rwork0.186 ---
all-68175 --
obs-56981 83.6 %-
Displacement parametersBiso mean: 32.9 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 11 440 4999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.78
LS refinement shellResolution: 1.75→1.81 Å
RfactorNum. reflection
Rfree0.346 233
Rwork0.295 -

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