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- PDB-4eiv: 1.37 Angstrom resolution crystal structure of apo-form of a putat... -

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Basic information

Entry
Database: PDB / ID: 4eiv
Title1.37 Angstrom resolution crystal structure of apo-form of a putative deoxyribose-phosphate aldolase from Toxoplasma gondii ME49
ComponentsDeoxyribose-phosphate aldolase
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
BETA-MERCAPTOETHANOL / deoxyribose-phosphate aldolase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Refinement description
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Mar 4, 2015Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyribose-phosphate aldolase
B: Deoxyribose-phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9688
Polymers64,6702
Non-polymers2986
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-64 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.982, 73.284, 96.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Deoxyribose-phosphate aldolase /


Mass: 32334.863 Da / Num. of mol.: 2 / Fragment: UNP residues 6-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: Toxoplasma gondii ME49 / Gene: TGGT1_122370, TGME49_118750, TGVEG_010130 / Plasmid: pCCK-N-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Magic / References: UniProt: B9PVB4, deoxyribose-phosphate aldolase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 1.97 Å3/Da / Density % sol: 37.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: The PACT suite B7(#19)-0.2 M NaCl, 0.1 M MES pH 6.0, 20% (w/v) PEG 6k. Protein at 12.7 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2012 / Details: Be-Lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. all: 107282 / Num. obs: 107282 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.99
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.86 / % possible all: 100

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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: PDB entry 3QYQ

3qyq


Resolution: 1.37→29.42 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.165 / SU ML: 0.039 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18485 5325 5 %RANDOM
Rwork0.15158 ---
obs0.15327 101562 99.41 %-
all-101562 --
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: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2---1.52 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.37→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 12 688 4583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224305
X-RAY DIFFRACTIONr_bond_other_d0.0010.022939
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9675852
X-RAY DIFFRACTIONr_angle_other_deg0.9033.0017180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0025581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0123.846182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.38715762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2211535
X-RAY DIFFRACTIONr_chiral_restr0.0830.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024984
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02891
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_it1.1811.52758
X-RAY DIFFRACTIONr_mcbond_other0.3811.51139
X-RAY DIFFRACTIONr_mcangle_it1.84724473
X-RAY DIFFRACTIONr_scbond_it2.97531547
X-RAY DIFFRACTIONr_scangle_it4.3934.51379
X-RAY DIFFRACTIONr_rigid_bond_restr1.13637244
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 400 -
Rwork0.208 7479 -
obs--100 %
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)
10.59730.5086-0.11123.308-0.32630.61250.0767-0.0546-0.02820.4858-0.08030.118-0.1237-0.01020.00360.0821-0.00870.02140.08030.00210.049-23.3251-0.964416.0914
20.68580.3152-0.31172.2088-0.76941.31620.0964-0.17050.00410.4182-0.0861-0.1651-0.14620.1181-0.01030.0842-0.0315-0.03930.1101-0.00030.0862-12.401712.777910.8998
31.1370.2675-0.30532.7203-0.53252.52340.00110.10630.0105-0.1597-0.0175-0.0895-0.01150.09210.01640.01070.0033-0.00060.11810.01380.1172-11.49298.9763-6.1908
42.23740.7753-0.5524.91290.89782.37870.01450.1952-0.005-0.283-0.0138-0.21360.0269-0.0185-0.00060.03210.0062-0.00640.09020.010.0839-19.6779-0.2188-6.1729
50.720.36430.06311.9261-0.74870.99210.0211-0.0688-0.00210.1262-0.04270.01350.026-0.06730.02170.02940.00040.00040.1036-0.00380.1048-22.8147-6.51947.3599
60.2962-0.4515-0.23092.26270.59270.35130.03270.01730.0077-0.1232-0.04720.11080.0111-0.07040.01450.0293-0.0014-0.01270.07790.00180.0788-20.2024-34.22940.2347
70.6372-0.05220.83450.97090.06143.7208-0.0011-0.0259-0.05090.00210.0005-0.09410.2793-0.01830.00060.03050.00590.01170.06510.00690.095-8.8089-42.34787.8572
81.079-0.0899-0.1791.8551-0.02252.4354-0.0074-0.098-0.04710.1775-0.0141-0.14950.06030.14270.02150.01920.0031-0.01730.08780.00810.089-5.337-36.58719.6814
92.75280.21150.14562.68930.56342.0025-0.009-0.12740.01320.2489-0.0005-0.1149-0.0183-0.02160.00960.03870.0039-0.01320.05170.01420.0427-14.4155-29.002722.1545
100.8329-0.16080.26581.4258-0.08151.619-0.00590.024-0.02930.00840.00720.075-0.0642-0.0791-0.00130.00280.00020.00010.06360.00070.0711-20.8958-24.88759.609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 50
2X-RAY DIFFRACTION2A51 - 114
3X-RAY DIFFRACTION3A115 - 173
4X-RAY DIFFRACTION4A174 - 200
5X-RAY DIFFRACTION5A219 - 278
6X-RAY DIFFRACTION6B0 - 60
7X-RAY DIFFRACTION7B61 - 119
8X-RAY DIFFRACTION8B120 - 172
9X-RAY DIFFRACTION9B173 - 201
10X-RAY DIFFRACTION10B202 - 276

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