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- PDB-5tkl: Crystal structure of FBP aldolase from Toxoplasma gondii, condens... -

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Basic information

Entry
Database: PDB / ID: 5tkl
TitleCrystal structure of FBP aldolase from Toxoplasma gondii, condensation intermediate
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / TIM BARREL / ALDOLASE / GLYCOLYSIS / SUBSTRATE / INTERMEDIATE / ENAMINE / COVALENT / SCHIFF BASE
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / actin binding / 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
1,3-DIHYDROXYACETONEPHOSPHATE / GLYCERALDEHYDE-3-PHOSPHATE / 1,6-di-O-phosphono-D-fructose / Fructose-bisphosphate aldolase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.751 Å
AuthorsHeron, P.W. / Sygusch, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Isomer activation controls stereospecificity of class I fructose-1,6-bisphosphate aldolases.
Authors: Heron, P.W. / Sygusch, J.
History
DepositionOct 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8274
Polymers39,1471
Non-polymers6803
Water5,945330
1
A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,30816
Polymers156,5874
Non-polymers2,72112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area14760 Å2
ΔGint-75 kcal/mol
Surface area46580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.621, 109.621, 54.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

21A-782-

HOH

31A-798-

HOH

41A-803-

HOH

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Components

#1: Protein Fructose-bisphosphate aldolase


Mass: 39146.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: ald-1 / Plasmid: pE-SUMO-AMP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star (DE3) / References: UniProt: Q8I8I2, fructose-bisphosphate aldolase
#2: Chemical ChemComp-P6F / 1,6-di-O-phosphono-D-fructose


Mass: 340.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O12P2
#3: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Chemical ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium Acetate, 0.2M Lithium Sulfate, 3.5% PEG 8000, 10% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 34234 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 23.91 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.066 / Χ2: 1.031 / Net I/av σ(I): 37.521 / Net I/σ(I): 13.8 / Num. measured all: 427202
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.75-1.787.216830.6110.4040.89899.6
1.78-1.818.716480.7520.3020.95899.20.8450.899
1.81-1.8510.516800.8790.2030.9899.90.6340.666
1.85-1.8911.217000.9150.1731.0041000.5620.589
1.89-1.9311.316610.950.1321.03999.80.430.451
1.93-1.9711.516950.9670.1061.0781000.350.366
1.97-2.0211.616820.9770.0861.01999.90.2860.3
2.02-2.0711.816940.9860.0651.01199.90.2170.226
2.07-2.1412.116810.9920.0511.0091000.1720.179
2.14-2.212.517040.9950.0420.95399.90.1450.151
2.2-2.2813.217000.9970.0340.931000.120.125
2.28-2.3813.816950.9980.0280.9221000.1010.105
2.38-2.4814.117070.9990.0230.9621000.0830.087
2.48-2.6114.317140.9990.021.0251000.0750.078
2.61-2.7814.517130.9990.0171.0831000.0620.064
2.78-2.9914.517200.9990.0151.2121000.0540.056
2.99-3.2914.417360.9990.0141.1061000.0510.053
3.29-3.7714.417440.9990.0130.9311000.0470.049
3.77-4.7514.217760.9990.011.1271000.0350.037
4.75-5013.319010.9990.0091.21899.90.0330.034

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Processing

Software
NameVersionClassification
PHENIXrefinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.751→49.129 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 2000 5.85 %
Rwork0.1485 32189 -
obs0.1502 34189 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.27 Å2 / Biso mean: 32.9261 Å2 / Biso min: 12.46 Å2
Refinement stepCycle: final / Resolution: 1.751→49.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 57 330 3044
Biso mean--52.99 42.72 -
Num. residues----350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052800
X-RAY DIFFRACTIONf_angle_d0.8043795
X-RAY DIFFRACTIONf_chiral_restr0.047419
X-RAY DIFFRACTIONf_plane_restr0.005496
X-RAY DIFFRACTIONf_dihedral_angle_d14.1571706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7514-1.79520.28641370.27992205234298
1.7952-1.84370.27471390.236222512390100
1.8437-1.8980.24761430.232222742417100
1.898-1.95920.25211400.205522752415100
1.9592-2.02930.22361410.179322582399100
2.0293-2.11050.21431410.159822862427100
2.1105-2.20660.16961420.14922682410100
2.2066-2.32290.1721410.137722742415100
2.3229-2.46840.18051420.134222882430100
2.4684-2.6590.16521440.133723082452100
2.659-2.92660.16421440.136623232467100
2.9266-3.34990.14471440.137923172461100
3.3499-4.22020.1661480.122323782526100
4.2202-49.14880.16171540.148824842638100
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)
11.23640.6142-0.23572.24010.38220.7469-0.13360.10520.1651-0.30350.18820.4469-0.2329-0.04590.01010.2035-0.0382-0.00740.17530.05090.2507-33.81663.1993-4.7781
20.97810.1933-0.00161.2743-0.06870.4751-0.01130.09780.0809-0.10790.0590.1596-0.005-0.04060.01260.14340.0005-0.01610.17060.02260.1284-20.63240.4742-7.0153
30.82830.471-0.24510.98560.55761.19920.00730.18470.0227-0.445-0.01180.4561-0.0295-0.0934-0.03980.2643-0.0353-0.11980.21430.0390.2674-34.8577-8.7054-15.3991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 83 )A1 - 83
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 277 )A84 - 277
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 363 )A278 - 363

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