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- PDB-1epx: CRYSTAL STRUCTURE ANALYSIS OF ALDOLASE FROM L. MEXICANA -

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Basic information

Entry
Database: PDB / ID: 1epx
TitleCRYSTAL STRUCTURE ANALYSIS OF ALDOLASE FROM L. MEXICANA
ComponentsFRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
KeywordsLYASE / beta barrel / pts signal / aldolase / leishmania / fructose-1 / 6-bisphosphate
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / cytoplasm
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 speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMar 29, 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: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)162,8944
Polymers162,8944
Non-polymers00
Water24,4101355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-43 kcal/mol
Surface area44540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.8, 118.1, 159.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40723.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: Q9U5N6, fructose-bisphosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1355 / 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: 2.4 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 13% mmePEG 5000, 50 mM sodium phosphate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 %(w/v)mPEG50001reservoir
250 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 139248 / Num. obs: 515238 / % possible obs: 92.9 % / Observed criterion σ(F): 20 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 14.95 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.53
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.087 / Num. unique all: 45455 / % possible all: 55
Reflection
*PLUS
Num. obs: 139238 / Num. measured all: 515238
Reflection shell
*PLUS
% possible obs: 55 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. Brucei Aldolase

Resolution: 1.8→20 Å / σ(F): 10000000 / σ(I): 2 / Stereochemistry target values: TNT ideal values
RfactorNum. reflection% reflectionSelection details
Rfree0.213 13934 9.28 %Used CNS
Rwork0.161 ---
all0.165 576473 --
obs0.175 515238 92.5 %-
Solvent computationSolvent model: Babinet Method / Bsol: 228.441 Å2 / ksol: 0.80209 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10776 0 0 1355 12131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.678
X-RAY DIFFRACTIONc_bond_d0.02
Refine LS restraints NCSWeight Biso : 2 / Weight position: 300
LS refinement shellResolution: 1.8→1.83 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.347 412 7.25 %
Rwork0.271 3652 -
obs--71.5 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: water.param
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.22 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS

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