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- PDB-4tr9: Ternary co-crystal structure of fructose-bisphosphate aldolase fr... -

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Basic information

Entry
Database: PDB / ID: 4tr9
TitleTernary co-crystal structure of fructose-bisphosphate aldolase from Plasmodium falciparum in complex with TRAP and a small molecule inhibitor
Components
  • ALA-ALA-ALA-SER-LEU-TYR-GLU-LYS-LYS-ALA-ALA
  • ALA-ALA-SER-LEU-TYR-GLU-LYS-LYS-ALA-ALA
  • ASP-TRP-ASN
  • Fructose-bisphosphate aldolase
KeywordsLyase/Lyase Inhibitor / Lyase-Lyase Inhibitor complex
Function / homology
Function and homology information


Fructose catabolism / Gluconeogenesis / Glycolysis / Platelet degranulation / microneme / Neutrophil degranulation / symbiont entry into host / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process ...Fructose catabolism / Gluconeogenesis / Glycolysis / Platelet degranulation / microneme / Neutrophil degranulation / symbiont entry into host / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / actin polymerization or depolymerization / glycolytic process / actin binding / host cell surface receptor binding / membrane / plasma membrane / cytosol / 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 / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain ...Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-38D / Thrombospondin-related anonymous protein / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.111 Å
AuthorsBosch, G. / Weltzer, R. / O'Malley, K. / Bosch, J.
Citation
Journal: Malar.J. / Year: 2015
Title: Inhibition by stabilization: targeting the Plasmodium falciparum aldolase-TRAP complex.
Authors: Nemetski, S.M. / Cardozo, T.J. / Bosch, G. / Weltzer, R. / O'Malley, K. / Ejigiri, I. / Kumar, K.A. / Buscaglia, C.A. / Nussenzweig, V. / Sinnis, P. / Levitskaya, J. / Bosch, J.
#1: Journal: J. Mol. Recognit. / Year: 2013
Title: Development of a multifunctional tool for drug screening against plasmodial protein-protein interactions via surface plasmon resonance
Authors: Boucher, L.E. / Bosch, J.
#2: Journal: MBio / Year: 2012
Title: Binding of aldolase and glyceraldehyde-3-phosphate dehydrogenase to the cytoplasmic tails of Plasmodium falciparum merozoite duffy binding-like and reticulocyte homology ligands.
Authors: Pal-Bhowmick, I. / Andersen, J. / Srinivasan, P. / Narum, D.L. / Bosch, J. / Miller, L.H.
#3: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2007
Title: Aldolase provides an unusual binding site for thrombospondin-related anonymous protein in the invasion machinery of the malaria parasite
Authors: Bosch, J. / Buscaglia, C.A. / Krumm, B. / Ingason, B.P. / Lucas, R. / Roach, C. / Cardozo, T. / Nussenzweig, V. / Hol, W.G.
History
DepositionJun 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
E: ALA-ALA-SER-LEU-TYR-GLU-LYS-LYS-ALA-ALA
G: ALA-ALA-ALA-SER-LEU-TYR-GLU-LYS-LYS-ALA-ALA
H: ASP-TRP-ASN
I: ASP-TRP-ASN
J: ASP-TRP-ASN
K: ASP-TRP-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,82314
Polymers164,52310
Non-polymers1,3014
Water10,881604
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16610 Å2
ΔGint-60 kcal/mol
Surface area50250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.896, 139.557, 142.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS A TETRAMER OF CHAINS A,B,C,D

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Fructose-bisphosphate aldolase /


Mass: 40152.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF14_0425 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KQL9, fructose-bisphosphate aldolase

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Protein/peptide , 3 types, 6 molecules EGHIJK

#2: Protein/peptide ALA-ALA-SER-LEU-TYR-GLU-LYS-LYS-ALA-ALA


Mass: 1053.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: It seems as if this is the C-terminal tail of Aldolase, however no direct connectivity to either Chain A,B,C,D could be made. Amino acids were modeled as good as possible
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KQL9*PLUS
#3: Protein/peptide ALA-ALA-ALA-SER-LEU-TYR-GLU-LYS-LYS-ALA-ALA


Mass: 1124.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: It seems as if this is the C-terminal tail of Aldolase, however no direct connectivity to either Chain A,B,C,D could be made. Amino acids were modeled as good as possible
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KQL9*PLUS
#4: Protein/peptide
ASP-TRP-ASN


Mass: 433.416 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Synthetic TRAP-tail / Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q76NM2*PLUS

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Non-polymers , 2 types, 608 molecules

#5: Chemical
ChemComp-38D / N'-[(E)-(2,4-dichlorophenyl)methylidene]-3,4-dihydroxybenzohydrazide


Mass: 325.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H10Cl2N2O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.6 %
Preparation: Data completeness is 61.1% due to the geometry of the detector used
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.1 M MgCl / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.11→44.85 Å / Num. obs: 49244 / % possible obs: 61.09 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.07019 / Net I/σ(I): 21.47
Reflection shellResolution: 2.11→2.186 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.9098 / Mean I/σ(I) obs: 1.04 / % possible all: 8.08

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pc4

2pc4


Resolution: 2.111→44.85 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 2493 5.06 %random selection
Rwork0.2057 ---
obs0.2086 49227 61.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.111→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10899 0 84 604 11587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211381
X-RAY DIFFRACTIONf_angle_d0.50115462
X-RAY DIFFRACTIONf_dihedral_angle_d10.234264
X-RAY DIFFRACTIONf_chiral_restr0.0191765
X-RAY DIFFRACTIONf_plane_restr0.0031999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.111-2.15110.4612170.3281228X-RAY DIFFRACTION6
2.1511-2.1950.3985400.3216478X-RAY DIFFRACTION12
2.195-2.24280.3617400.3201688X-RAY DIFFRACTION17
2.2428-2.29490.286380.3312882X-RAY DIFFRACTION21
2.2949-2.35230.3744460.31151085X-RAY DIFFRACTION26
2.3523-2.41590.3279640.29091299X-RAY DIFFRACTION31
2.4159-2.4870.3317940.29021546X-RAY DIFFRACTION37
2.487-2.56730.3697900.28971878X-RAY DIFFRACTION44
2.5673-2.6590.30351030.28392265X-RAY DIFFRACTION53
2.659-2.76550.28351400.27082799X-RAY DIFFRACTION66
2.7655-2.89130.34371920.27483658X-RAY DIFFRACTION86
2.8913-3.04370.35322390.26954177X-RAY DIFFRACTION99
3.0437-3.23440.32450.24354175X-RAY DIFFRACTION99
3.2344-3.4840.29442250.21794227X-RAY DIFFRACTION99
3.484-3.83440.25862340.18944237X-RAY DIFFRACTION99
3.8344-4.38890.22972230.16614271X-RAY DIFFRACTION99
4.3889-5.52790.21412360.15974313X-RAY DIFFRACTION99
5.5279-44.850.20752270.17444528X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2126-0.20820.26390.21790.03530.29490.001-0.0573-0.07410.00740.00540.02980.03590.0608-00.2646-0.02520.03570.26660.0020.23131.8726-16.607719.0938
20.33760.07250.06950.1304-0.19930.2630.03870.0093-0.0220.0047-0.02130.03030.0233-0.099800.1054-0.0072-0.01520.1775-0.00560.16040.7246-7.47228.7691
30.06170.0297-0.149-0.00460.01160.2959-0.07380.24410.01180.09170.0099-0.0071-0.0231-0.0635-00.2569-0.0071-0.05280.3087-0.01450.3096-7.6997-6.543210.759
40.29380.04570.12540.22840.18760.70740.13370.1253-0.0106-0.1859-0.02240.02790.1583-0.04110.00190.3356-0.00680.00360.1936-0.0130.22757.4696-29.843359.5359
50.2082-0.11020.07810.10360.03520.1097-0.03750.0936-0.12830.076-0.0984-0.02790.50260.006-0.00380.2882-0.018-0.00570.19160.0570.27732.9235-38.837462.0144
60.19430.2872-0.1041-0.0255-0.20040.5043-0.0113-0.0035-0.01740.0616-0.01030.0394-0.02420.0051-00.19270.0327-0.00660.21420.01360.245410.0261-18.141148.1056
70.0037-0.08770.1030.28080.00850.27180.03590.1428-0.0476-0.0505-0.03740.03130.12310.0884-00.1291-0.0001-0.00910.23110.00580.217817.1297-12.726261.031
80.2360.2416-0.23520.2473-0.25780.24310.20060.0511-0.01070.075-0.295-0.0482-0.01670.1179-0.00580.26860.0621-0.03520.3092-0.00120.345419.5167-26.33568.6838
90.0547-0.0833-0.00640.0806-0.03440.07930.0659-0.0757-0.17340.2626-0.1756-0.16720.338-0.0411-00.3691-0.0114-0.03120.30030.03890.357418.3504-34.178474.0318
100.1840.1843-0.33950.2608-0.28360.3496-0.15980.09850.1265-0.05620.1169-0.0557-0.18960.191-0.01140.3015-0.0269-0.0540.270.03530.196212.663414.765970.0833
110.31730.1619-0.21320.1215-0.1530.1552-0.0095-0.03350.10530.14940.02070.0428-0.28380.09940.00080.3409-0.009-0.0570.186-0.00730.23278.404528.44379.7244
120.21410.08120.02890.22580.24190.5139-0.0343-0.0263-0.0193-0.00370.00840.0261-0.1406-0.0542-00.1477-0.00410.00490.1841-0.00770.20212.910210.420664.1852
130.11860.07990.02630.38820.05860.05090.1032-0.36250.07990.2347-0.3488-0.0437-0.1109-0.0837-0.02640.24590.07770.02790.263-0.07270.3593-3.942321.050485.2706
140.07590.0893-0.05310.0269-0.03550.0029-0.0639-0.1851-0.0034-0.02930.0161-0.0938-0.1552-0.1398-0.00010.52930.0616-0.1550.34130.03620.4052-0.372720.49433.5513
150.02960.0733-0.00640.2117-0.01320.14240.1866-0.12750.29150.2644-0.06610.09850.32120.5410.0810.6162-0.2934-0.01690.7501-0.10830.312730.621833.125935.6707
160.2653-0.09290.12360.3220.06740.06950.047-0.07460.1855-0.15560.00380.0411-0.13480.15210.03950.3917-0.14990.01760.278-0.03220.25423.952738.226131.8025
171.0637-0.11760.35840.1642-0.12840.1810.31080.42370.4018-0.00220.25070.103-0.73490.45630.46210.7075-0.22310.10140.25360.00760.320318.555641.638131.2455
180.085-0.0741-0.10170.0334-0.09060.27460.0865-0.039-0.0856-0.0321-0.12130.1862-0.23570.155400.385-0.0620.01310.31-0.00510.353519.090221.242744.9062
190.02590.03470.010.2757-0.48670.4961-0.0173-0.0486-0.02460.0356-0.04250.0813-0.13950.146-0.00920.1789-0.0824-0.01450.2616-0.00630.186220.004612.407134.3617
200.73820.0797-0.08921.42620.52850.1748-0.2118-0.5855-0.1132-0.6189-0.08330.0961-0.37220.5336-0.15590.3167-0.24750.02020.4127-0.03330.160529.002823.733924.2994
210.3795-0.31210.27690.2789-0.24320.19170.512-0.2956-0.0133-0.477-0.414-0.4362-0.2987-0.09470.09030.5724-0.19650.17790.41220.0430.451730.644231.337418.7713
220.0445-0.00920.03290.0177-0.010.0227-0.0487-0.09510.2278-0.0022-0.180.0647-0.00840.25450.00010.26210.0467-0.08690.38230.03750.34172.588917.068117.003
230.0146-0.0186-0.01640.01560.01220.02430.1268-0.330.0796-0.07370.2486-0.0426-0.01540.1107-0.00011.0285-0.1296-0.08391.27350.03950.554717.8559-4.317878.7282
240.00070.00490.00460.02210.02120.0406-0.05850.1745-0.22350.08560.0705-0.076-0.1203-0.05420.00040.5709-0.0860.22491.1268-0.06330.8965-10.2344-11.920923.117
250.01880.0434-0.00170.0994-0.01410.022-0.0956-0.002-0.263-0.0471-0.17940.0715-0.2080.1016-01.0752-0.05290.28140.7152-0.3180.921420.806-28.283957.5021
260.01730.02020.01640.020.020.0410.00710.23220.08930.0060.2429-0.09510.1154-0.11140.00050.65970.00120.0460.5098-0.02170.7634-3.614121.229970.1765
270.0017-0.00790.00570.1066-0.02340.0182-0.1094-0.16850.19120.0616-0.01270.0695-0.0380.004501.157-0.1703-0.35020.8428-0.12980.968330.985525.120835.4422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 282 )
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 351 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 89 )
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 112 )
6X-RAY DIFFRACTION6chain 'B' and (resid 113 through 186 )
7X-RAY DIFFRACTION7chain 'B' and (resid 187 through 282 )
8X-RAY DIFFRACTION8chain 'B' and (resid 283 through 322 )
9X-RAY DIFFRACTION9chain 'B' and (resid 323 through 351 )
10X-RAY DIFFRACTION10chain 'C' and (resid 5 through 51 )
11X-RAY DIFFRACTION11chain 'C' and (resid 52 through 112 )
12X-RAY DIFFRACTION12chain 'C' and (resid 113 through 308 )
13X-RAY DIFFRACTION13chain 'C' and (resid 309 through 351 )
14X-RAY DIFFRACTION14chain 'D' and (resid 5 through 28 )
15X-RAY DIFFRACTION15chain 'D' and (resid 29 through 57 )
16X-RAY DIFFRACTION16chain 'D' and (resid 58 through 89 )
17X-RAY DIFFRACTION17chain 'D' and (resid 90 through 112 )
18X-RAY DIFFRACTION18chain 'D' and (resid 113 through 166 )
19X-RAY DIFFRACTION19chain 'D' and (resid 167 through 282 )
20X-RAY DIFFRACTION20chain 'D' and (resid 283 through 322 )
21X-RAY DIFFRACTION21chain 'D' and (resid 323 through 351 )
22X-RAY DIFFRACTION22chain 'E' and (resid 7 through 16 )
23X-RAY DIFFRACTION23chain 'G' and (resid 6 through 16 )
24X-RAY DIFFRACTION24chain 'H' and (resid 604 through 606 )
25X-RAY DIFFRACTION25chain 'I' and (resid 604 through 606 )
26X-RAY DIFFRACTION26chain 'J' and (resid 604 through 606 )
27X-RAY DIFFRACTION27chain 'K' and (resid 604 through 606 )

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