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- PDB-3qyq: 1.8 Angstrom resolution crystal structure of a putative deoxyribo... -

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Entry
Database: PDB / ID: 3qyq
Title1.8 Angstrom resolution crystal structure of a putative deoxyribose-phosphate aldolase from Toxoplasma gondii ME49
ComponentsDeoxyribose-phosphate aldolase, putative
KeywordsLYASE / Chemotherapy / Brain Cysts / Bradyzoite / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM-barrel
Function / homology
Function and homology information


deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / cytoplasm
Similarity search - Function
Deoxyribose-phosphate aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
sucrose / 2-deoxy-D-ribose 5-phosphate aldolase / deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHalavaty, A.S. / Ruan, J. / Minasov, G. / Shuvalova, L. / Ueno, A. / Igarashi, M. / Ngo, H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
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
DepositionMar 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Refinement description
Revision 1.3Nov 12, 2014Group: Database references
Revision 1.4Apr 8, 2015Group: Database references
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Deoxyribose-phosphate aldolase, putative
B: Deoxyribose-phosphate aldolase, putative
C: Deoxyribose-phosphate aldolase, putative
D: Deoxyribose-phosphate aldolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,20623
Polymers127,6424
Non-polymers2,56419
Water16,700927
1
A: Deoxyribose-phosphate aldolase, putative
C: Deoxyribose-phosphate aldolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,27412
Polymers63,8212
Non-polymers1,45310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-126 kcal/mol
Surface area23790 Å2
MethodPISA
2
B: Deoxyribose-phosphate aldolase, putative
D: Deoxyribose-phosphate aldolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,93211
Polymers63,8212
Non-polymers1,1119
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-139 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.923, 72.194, 73.048
Angle α, β, γ (deg.)62.90, 89.80, 88.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Deoxyribose-phosphate aldolase, putative


Mass: 31910.422 Da / Num. of mol.: 4 / Fragment: UNP residues 6-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGME49_118750 / Plasmid: pCCK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic
References: UniProt: B6KPX4, UniProt: B9PVB4*PLUS, deoxyribose-phosphate aldolase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 927 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Protein at 7 mg/mL in 10 mM Tris/HCl, pH=8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: 0.1 M Citric acid, pH=4.0, 0.8 M Ammonium sulfate (The AmSO4 suite, condition E1 (49)). Cryo ...Details: Protein at 7 mg/mL in 10 mM Tris/HCl, pH=8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: 0.1 M Citric acid, pH=4.0, 0.8 M Ammonium sulfate (The AmSO4 suite, condition E1 (49)). Cryo condition: 1:1 v/v 50 % sucrose:E1 condition , VAPOR DIFFUSION, SITTING DROP, temperature 277 and 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2011 / Details: Be-Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 116483 / Num. obs: 116483 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.66
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.36 / % possible all: 96.2

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A4A

2a4a


Resolution: 1.8→29.49 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.192 / SU ML: 0.073 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 5879 5 %RANDOM
Rwork0.16568 ---
obs0.1674 110552 97.26 %-
all-110552 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.566 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å2-0.87 Å21.07 Å2
2--1.22 Å2-0.91 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8272 0 149 927 9348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229152
X-RAY DIFFRACTIONr_bond_other_d0.0010.026163
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9812467
X-RAY DIFFRACTIONr_angle_other_deg0.827315071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.48151215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.7323.883394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.081151596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1771576
X-RAY DIFFRACTIONr_chiral_restr0.1010.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021881
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_it1.0341.55767
X-RAY DIFFRACTIONr_mcbond_other0.2981.52386
X-RAY DIFFRACTIONr_mcangle_it1.89629349
X-RAY DIFFRACTIONr_scbond_it3.06933385
X-RAY DIFFRACTIONr_scangle_it5.1024.53118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 384 -
Rwork0.241 7771 -
obs--92.37 %
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)
10.3698-0.2917-0.4420.45730.55321.06080.0112-0.00720.044-0.013-0.0155-0.048-0.0939-0.02490.00420.01880.0067-0.00760.01030.01140.044719.461678.800731.9444
20.6882-0.3851-0.04841.34310.04390.7823-0.0492-0.10760.03760.18270.01280.09010.0961-0.14020.03640.0364-0.01130.01950.0668-0.00660.02086.694866.473647.5874
35.79871.01770.6340.4324-0.07390.2275-0.22150.0007-0.0701-0.07990.1813-0.01750.0449-0.12980.04030.132-0.06450.0430.14770.01570.08562.270652.5136.6592
40.5680.1948-0.24620.4798-0.11410.82040.004-0.03260.03630.0512-0.018-0.00630.0312-0.02040.0140.0079-0.0029-0.00060.01280.00920.021220.151566.444729.6742
50.40860.0025-0.28140.28990.25140.5890.0355-0.00390.0391-0.0749-0.01310.0457-0.1674-0.0107-0.02240.0587-0.00060.00090.01080.01180.036346.818394.70576.1311
60.7597-0.1612-0.42120.64050.35870.854-0.03980.0041-0.07120.0901-0.01060.03560.04430.08570.05040.0142-0.00560.00320.03490.02670.049845.905277.42715.1272
74.7051.98310.19351.1345-0.47592.1497-0.12280.3886-0.3015-0.0180.1554-0.0676-0.04910.0606-0.03260.0099-0.00660.01370.0514-0.01210.060637.155668.11913.8259
80.3373-0.3044-0.31120.45160.09771.00170.0054-0.01290.0187-0.06310.02820.0201-0.04010.0113-0.03360.0392-0.0151-0.01870.0180.01070.013154.620385.9415-2.4518
90.59280.32970.8490.76520.76191.66710.0786-0.0042-0.08050.0473-0.0204-0.02350.2126-0.0021-0.05810.05540.0021-0.01390.00130.00360.043418.86846.463110.7216
100.42540.18840.11960.92080.26191.05520.04550.03130.0196-0.1225-0.05950.0274-0.0124-0.05130.0140.03720.0261-0.01160.04590.00010.025111.710260.1483-6.9006
117.1835-2.0793-0.32350.62380.06610.0550.0091-0.01620.011-0.0185-0.01190.00140.0120.00740.00280.02130.0232-0.02330.06330.01330.08418.298674.70614.7347
120.437-0.0560.02450.2856-0.07410.90650.02010.057-0.00360.0008-0.0329-0.01630.0906-0.0190.01280.01520.0021-0.00980.01910.00640.039621.973258.754714.0392
130.39830.29470.38190.85680.79361.02550.05120.0144-0.08540.08780.06-0.06990.1190.1232-0.11120.03680.0179-0.01780.0310.00110.042556.46566.2077-22.0893
140.45830.08410.02980.96770.15050.5742-0.0028-0.0078-0.0036-0.0364-0.03460.08-0.06880.01020.03740.04030.0092-0.01520.00950.00390.02742.255575.9327-37.5972
156.3164-0.0371-1.44020.6919-0.30490.595-0.2321-0.05590.03950.0930.1610.0528-0.0306-0.01420.07110.07260.018-0.02470.05650.04690.086136.238487.7497-25.7052
160.22340.14940.50840.50710.38181.1747-0.04730.0096-0.0153-0.03540.0722-0.0557-0.10520.0423-0.02490.0372-0.00210.00180.02540.00730.022255.724579.2075-19.0817
170.16440.07221.04170.03490.46046.609-0.09360.02640.03310.004-0.06270.017-0.20990.15980.15620.1825-0.1010.00650.1514-0.02620.072857.1308102.328210.5243
184.8441-3.95831.92543.2347-1.57340.7672-0.1941-0.02750.23870.18540.057-0.1977-0.0836-0.0030.13710.1028-0.00930.00150.14930.00240.10526.381581.821343.3237
1956.2595-9.2368-0.613762.07098.40641.1469-0.3033-0.2771-0.5943-0.15060.5288-2.0995-0.02930.0715-0.22540.1627-0.0213-0.06270.12420.07520.171919.03467.128958.1939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 0
2X-RAY DIFFRACTION1A6 - 76
3X-RAY DIFFRACTION2A77 - 185
4X-RAY DIFFRACTION3A186 - 210
5X-RAY DIFFRACTION4A218 - 279
6X-RAY DIFFRACTION5B-4 - 0
7X-RAY DIFFRACTION5B6 - 113
8X-RAY DIFFRACTION6B114 - 195
9X-RAY DIFFRACTION7B196 - 219
10X-RAY DIFFRACTION8B220 - 277
11X-RAY DIFFRACTION9C-3 - 0
12X-RAY DIFFRACTION9C6 - 76
13X-RAY DIFFRACTION10C77 - 182
14X-RAY DIFFRACTION11C183 - 219
15X-RAY DIFFRACTION12C220 - 280
16X-RAY DIFFRACTION13D-3 - 74
17X-RAY DIFFRACTION14D75 - 182
18X-RAY DIFFRACTION15D183 - 219
19X-RAY DIFFRACTION16D220 - 280
20X-RAY DIFFRACTION17B1
21X-RAY DIFFRACTION18A2
22X-RAY DIFFRACTION19A3

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