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- PDB-4d2j: Crystal structure of F16BP Aldolase from Toxoplasma gondii (TgALD1) -

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Basic information

Entry
Database: PDB / ID: 4d2j
TitleCrystal structure of F16BP Aldolase from Toxoplasma gondii (TgALD1)
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE
KeywordsLYASE / APICOMPLEXA / TIM BARREL / GLYCOLYSIS
Function / homology
Function and homology information


apical cytoplasm / biological process involved in symbiotic interaction / adhesion of symbiont to host cell / symbiont entry into host / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / positive regulation of ATP biosynthetic process / glycolytic process / actin filament binding ...apical cytoplasm / biological process involved in symbiotic interaction / adhesion of symbiont to host cell / symbiont entry into host / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / positive regulation of ATP biosynthetic process / glycolytic process / actin filament binding / positive regulation of cell population proliferation / extracellular space / membrane
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
ACETATE ION / BETA-MERCAPTOETHANOL / Fructose-bisphosphate aldolase / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTonkin, M.L. / Ramaswamy, R. / Halavaty, A.S. / Ruan, J. / Igarashi, M. / Ngo, H.M. / Boulanger, M.J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structural and Functional Divergence of the Aldolase Fold in Toxoplasma Gondii.
Authors: Tonkin, M.L. / Halavaty, A.S. / Ramaswamy, R. / Ruan, J. / Igarashi, M. / Ngo, H.M. / Boulanger, M.J.
History
DepositionMay 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)38,3037
Polymers37,8221
Non-polymers4806
Water3,333185
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)153,21128
Polymers151,2894
Non-polymers1,92224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_554-y,-x,-z-11
crystal symmetry operation7_554y,x,-z-11
Buried area11630 Å2
ΔGint-143.5 kcal/mol
Surface area48770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.814, 109.814, 54.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FRUCTOSE-BISPHOSPHATE ALDOLASE / ALDOLASE 1


Mass: 37822.301 Da / Num. of mol.: 1 / Fragment: F16BP ALDOLASE, RESIDUES 7-422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: S8GE25, UniProt: B9PW35*PLUS, fructose-bisphosphate aldolase

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Non-polymers , 5 types, 191 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.17 Å3/Da / Density % sol: 43.33 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M SODIUM CHLORIDE, 0.1 M HEPES PH 7.5, 1.6 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 33917 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 44
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KX6

3kx6


Resolution: 1.75→36.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.866 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23073 1718 5.1 %RANDOM
Rwork0.19014 ---
obs0.19218 32144 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.612 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 28 185 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192642
X-RAY DIFFRACTIONr_bond_other_d0.0010.022584
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.993564
X-RAY DIFFRACTIONr_angle_other_deg0.70335967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41424.393107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66615464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0261516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.972.9471355
X-RAY DIFFRACTIONr_mcbond_other2.9372.9431352
X-RAY DIFFRACTIONr_mcangle_it3.7194.4011690
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5933.3121286
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 124 -
Rwork0.238 2323 -
obs--100 %

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