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- PDB-1a5c: FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM PLASMODIUM FALCIPARUM -

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Basic information

Entry
Database: PDB / ID: 1a5c
TitleFRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM PLASMODIUM FALCIPARUM
ComponentsFRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
KeywordsLYASE / FRUCTOSE-1 / 6-BISPHOSPHATE ALDOLASE / MALARIA / TIM BARREL
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / actin binding / host cell plasma membrane / membrane / 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 speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKim, H. / Certa, U. / Dobeli, H. / Jakob, P. / Hol, W.G.J.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of fructose-1,6-bisphosphate aldolase from the human malaria parasite Plasmodium falciparum.
Authors: Kim, H. / Certa, U. / Dobeli, H. / Jakob, P. / Hol, W.G.
History
DepositionFeb 13, 1998Processing site: BNL
Revision 1.0Jun 10, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)80,0432
Polymers80,0432
Non-polymers00
Water00
1
A: FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
B: FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE

A: FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
B: FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE


Theoretical massNumber of molelcules
Total (without water)160,0874
Polymers160,0874
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+4/31
Unit cell
Length a, b, c (Å)119.200, 119.200, 132.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99998, 0.000661, -0.006211), (0.00576, -0.286989, -0.957917), (-0.002416, -0.957934, 0.28698)
Vector: 22.8268, 217.282, 161.5977)

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Components

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


Mass: 40021.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: P14223, fructose-bisphosphate aldolase

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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: 3.39 Å3/Da / Density % sol: 63.7 %
Crystal growMethod: vapor diffusion / pH: 7.6
Details: VAPOR DIFFUSION: 2.0 M AMMONIUM SULFATE/5% 2-PROPANOL, pH 7.6, vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate1reservoir
25 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9
DetectorDate: Oct 26, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 20677 / % possible obs: 94 % / Rsym value: 0.077 / Net I/σ(I): 8.2
Reflection shellResolution: 3→3.08 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.175

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
XDSdata reduction
XDSdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FBA

1fba


Resolution: 3→8 Å / Cross valid method: THROUGHOUT
Details: TWO-FOLD NCS-RESTRAINTS FOR 4 PGKS AT 2.8 A RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.329 830 5 %RANDOM
Rwork0.239 ---
obs0.239 17162 94 %-
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5202 0 0 0 5202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.13 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.499 66 4.5 %
Rwork0.33 1569 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor obs: 0.33

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