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- PDB-5tjs: Crystal structure of FBP aldolase from Toxoplasma gondii, native form -

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Basic information

Entry
Database: PDB / ID: 5tjs
TitleCrystal structure of FBP aldolase from Toxoplasma gondii, native form
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / TIM BARREL / ALDOLASE / GLYCOLYSIS
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / 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
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 5, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2392
Polymers39,1471
Non-polymers921
Water5,981332
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)156,9568
Polymers156,5874
Non-polymers3684
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 area12480 Å2
ΔGint-47 kcal/mol
Surface area47520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.218, 110.218, 54.921
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-785-

HOH

21A-813-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
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: 1.78→50 Å / Num. obs: 32711 / % possible obs: 99.1 % / Redundancy: 13.4 % / Biso Wilson estimate: 24.54 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.083 / Χ2: 0.968 / Net I/av σ(I): 29.878 / Net I/σ(I): 9.3 / Num. measured all: 438181
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.78-1.818.714300.5160.4770.76387.8
1.81-1.849.415080.6220.4120.8494
1.84-1.8810.516180.7450.3130.8871000.986
1.88-1.9212.816130.8880.220.92399.90.7670.798
1.92-1.9613.416300.9310.1720.9481000.6130.637
1.96-213.616230.9420.1461.06999.90.5250.545
2-2.0513.616180.9660.1091.02399.90.3920.407
2.05-2.1113.716390.9780.0840.9881000.3040.315
2.11-2.1713.916170.9890.0680.9591000.2480.257
2.17-2.2414.116420.9920.0580.9441000.2120.22
2.24-2.3214.216450.9950.0460.8641000.1680.175
2.32-2.4214.516280.9970.0380.8261000.1410.146
2.42-2.5314.616310.9980.0310.8561000.1140.118
2.53-2.6614.616480.9980.0270.8681000.1010.104
2.66-2.8314.516590.9980.0210.9251000.0790.082
2.83-3.0414.516610.9990.0180.9991000.0650.068
3.04-3.3514.516630.9990.0151.1951000.0550.057
3.35-3.8314.416910.9990.0141.0181000.0510.053
3.83-4.8314.217180.9990.0111.0431000.0390.041
4.83-5013.318290.9990.011.23399.80.0360.038

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Processing

Software
NameVersionClassification
PHENIXrefinement
CBASSdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QUT
Resolution: 1.78→38.968 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1981 2000 6.12 %
Rwork0.1547 30662 -
obs0.1572 32662 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.96 Å2 / Biso mean: 36.7027 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 1.78→38.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 14 332 2990
Biso mean--70.68 43.98 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092709
X-RAY DIFFRACTIONf_angle_d1.1973660
X-RAY DIFFRACTIONf_chiral_restr0.052407
X-RAY DIFFRACTIONf_plane_restr0.007477
X-RAY DIFFRACTIONf_dihedral_angle_d13.5691018
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 (%)
1.7801-1.82470.33381240.29521899202388
1.8247-1.8740.3171400.25032147228798
1.874-1.92910.2481420.21721602302100
1.9291-1.99140.23221410.21321822323100
1.9914-2.06260.25221420.18721652307100
2.0626-2.14510.20031420.166721902332100
2.1451-2.24280.17581430.156421892332100
2.2428-2.3610.21891440.14622082352100
2.361-2.50890.19281430.141122052348100
2.5089-2.70260.19191430.142721892332100
2.7026-2.97440.20381450.14722122357100
2.9744-3.40460.1891470.149522542401100
3.4046-4.28860.16351480.128222652413100
4.2886-38.97730.18781560.147123972553100
Refinement TLS params.Method: refined / Origin x: -26.6042 Å / Origin y: -0.8177 Å / Origin z: -8.0459 Å
111213212223313233
T0.1698 Å20.0023 Å2-0.0356 Å2-0.2025 Å20.0692 Å2--0.2028 Å2
L1.1361 °20.4005 °20.1461 °2-1.7481 °20.1191 °2--0.4826 °2
S-0.0205 Å °0.128 Å °0.1376 Å °-0.1581 Å °0.0854 Å °0.3985 Å °0.0179 Å °-0.0679 Å °-0.0518 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 363
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allS1 - 366

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