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- PDB-5tkp: Crystal structure of FBP aldolase from Toxoplasma gondii, equilib... -

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Basic information

Entry
Database: PDB / ID: 5tkp
TitleCrystal structure of FBP aldolase from Toxoplasma gondii, equilibrium Schiff base FBP complex
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / TIM BARREL / ALDOLASE / GLYCOLYSIS / SUBSTRATE / INTERMEDIATE / COVALENT / SCHIFF BASE
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
1,6-di-O-phosphono-D-fructose / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesToxoplasma gondii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.09 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4872
Polymers39,1471
Non-polymers3401
Water3,711206
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)157,9488
Polymers156,5874
Non-polymers1,3604
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 area11420 Å2
ΔGint-46 kcal/mol
Surface area47070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.120, 109.120, 54.800
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-700-

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 (unknown) / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
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: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 19184 / % possible obs: 95.1 % / Redundancy: 8 % / Biso Wilson estimate: 30.45 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Rrim(I) all: 0.087 / Χ2: 0.881 / Net I/av σ(I): 19.846 / Net I/σ(I): 8.4 / Num. measured all: 154302
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.09-2.133.30.8830.491161.6
2.13-2.1640.960.578172.4
2.16-2.214.40.8360.623181
2.21-2.255.20.7290.772190.5
2.25-2.36.30.6760.825195.7
2.3-2.3570.6120.863199.3
2.35-2.417.30.5160.9199.8
2.41-2.4870.4390.927199.9
2.48-2.5580.3870.951199.7
2.55-2.6380.3290.959199.8
2.63-2.737.70.2620.968199.9
2.73-2.848.70.2180.9841100
2.84-2.978.80.1790.9891100
2.97-3.128.30.1290.9931100
3.12-3.328.80.10.9961100
3.32-3.579.10.070.998199.9
3.57-3.9310.40.0520.9991100
3.93-4.510.90.0420.9991100
4.5-5.6711.50.0390.9991100
5.67-50110.040.999199.9

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Processing

Software
NameVersionClassification
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.09→50 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.81
RfactorNum. reflection% reflection
Rfree0.2113 1341 7.68 %
Rwork0.1604 --
obs0.1643 17454 86.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.79 Å2 / Biso mean: 39.2937 Å2 / Biso min: 17.22 Å2
Refinement stepCycle: final / Resolution: 2.09→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 29 206 2884
Biso mean--58.46 39.33 -
Num. residues----349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062727
X-RAY DIFFRACTIONf_angle_d0.9423691
X-RAY DIFFRACTIONf_chiral_restr0.039411
X-RAY DIFFRACTIONf_plane_restr0.004480
X-RAY DIFFRACTIONf_dihedral_angle_d13.461024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.16470.30021240.24111478160282
2.1647-2.25140.27011230.22371482160581
2.2514-2.35390.27341210.21781454157580
2.3539-2.4780.26951210.20531449157079
2.478-2.63320.2461170.17821418153578
2.6332-2.83650.21621180.16771420153877
2.8365-3.1220.23641370.15791645178289
3.122-3.57360.22321550.14211857201299
3.5736-4.50210.16351590.121418992058100
4.5021-54.57860.1831660.162420112177100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.65330.6429-0.55822.11190.65171.2265-0.03880.06150.1431-0.21560.16810.4009-0.144-0.09640.00010.2692-0.02520.01970.27140.02710.3469-34.2343.4343-4.814
21.52280.213-0.03751.3812-0.09520.418-0.03120.10320.0738-0.15130.05920.16720.0043-0.01850.00080.2396-0.0024-0.02950.23190.02020.1934-22.5129-1.1206-8.5344
30.36550.4086-0.01230.61840.35260.82520.25060.3445-0.0272-0.4958-0.24780.34720.2044-0.1638-0.00010.3717-0.0309-0.09670.35220.03390.4952-38.03-9.5391-15.8465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 84 )A2 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 317 )A85 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 363 )A318 - 363

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