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- PDB-1f2j: CRYSTAL STRUCTURE ANALYSIS OF ALDOLASE FROM T. BRUCEI -

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Basic information

Entry
Database: PDB / ID: 1f2j
TitleCRYSTAL STRUCTURE ANALYSIS OF ALDOLASE FROM T. BRUCEI
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE, GLYCOSOMAL
KeywordsLYASE / BETA BARREL / PTS SIGNAL / ALDOLASE / TRYPANOSOMA / FRUCTOSE 1 / 6 BISPHOSPHATE
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycosome / glycolytic process
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, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChudzik, D.M. / Michels, P.A. / De Walque, S. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structures of type 2 peroxisomal targeting signals in two trypanosomatid aldolases.
Authors: Chudzik, D.M. / Michels, P.A. / de Walque, S. / Hol, W.G.
History
DepositionMay 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 6, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_assembly_prop.biol_id
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE, GLYCOSOMAL


Theoretical massNumber of molelcules
Total (without water)40,9401
Polymers40,9401
Non-polymers00
Water4,342241
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE, GLYCOSOMAL

A: FRUCTOSE-BISPHOSPHATE ALDOLASE, GLYCOSOMAL

A: FRUCTOSE-BISPHOSPHATE ALDOLASE, GLYCOSOMAL

A: FRUCTOSE-BISPHOSPHATE ALDOLASE, GLYCOSOMAL


Theoretical massNumber of molelcules
Total (without water)163,7604
Polymers163,7604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation37_546y+1/2,x-1/2,-z+3/21
crystal symmetry operation38_556-y+1/2,-x+1/2,-z+3/21
Buried area12680 Å2
ΔGint-54 kcal/mol
Surface area45860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.660, 209.660, 209.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein FRUCTOSE-BISPHOSPHATE ALDOLASE, GLYCOSOMAL / / FRUCTOSE-1 / 6-BISPHOSPHATE ALDOLASE


Mass: 40939.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P07752, fructose-bisphosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 4.7 Å3/Da / Density % sol: 73.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 100 mM sodium acetate pH 4.9, 1.9 M ammonium sulfate, 20 mM L-cysteine, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
220 mMHEPES1drop
3100 mM1dropNaCl
41 mMdithiothreitol1drop
5100 mMPMSF1drop
61.9 Mammonium sulfate1reservoir
720 mML-cysteine1reservoir
8100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→84.5 Å / Num. all: 29298 / Num. obs: 479727 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.3
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.121 / Num. unique all: 5143 / % possible all: 72.1
Reflection
*PLUS
Num. obs: 29298 / Num. measured all: 479727
Reflection shell
*PLUS
% possible obs: 72.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TETRAMERIC RABBIT ALDOLASE (1ADO)

1ado


Resolution: 1.9→15 Å / σ(F): 10000000 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 5960 9.86 %RANDOM
Rwork0.199 ---
all0.199 29298 --
obs0.199 59600 --
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 0 241 2948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.034
X-RAY DIFFRACTIONx_angle_deg4.084
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.353 638 9.1 %
Rwork0.293 5700 -
obs--99.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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