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- PDB-8gjb: L-threonine 3-Dehydrogenase from Trypanosoma cruzi in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8gjb
TitleL-threonine 3-Dehydrogenase from Trypanosoma cruzi in complex with NAD and acetate
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / threonine / dehydrogenase / trypanossoma / NAD / complex / potassium
Function / homology: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / ACETATE ION / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-threonine 3-dehydrogenase, putative
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMercaldi, G.F. / Faria, J.N. / Fagundes, M. / Bezerra, E.H.S. / Cordeiro, A.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/22202-8 Brazil
Sao Paulo Research Foundation (FAPESP)2021/14741-9 Brazil
CitationJournal: To Be Published
Title: Structure, allosteric regulation and metabolic activity of L-threonine 3-Dehydrogenase from Trypanosoma cruzi
Authors: Faria, J.N. / Mercaldi, G.F. / Fagundes, M. / Eufrasio, A.G. / Cordeiro, A.T.
History
DepositionMar 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,92411
Polymers81,0072
Non-polymers1,9179
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-37 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.274, 82.733, 84.384
Angle α, β, γ (deg.)90.000, 90.446, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-threonine 3-dehydrogenase


Mass: 40503.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053507923.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4CU39, L-threonine 3-dehydrogenase

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Non-polymers , 6 types, 294 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 0.2 M Ammonium acetate, 0.1 M Bis-Tris (pH 5.3), 25% PEG 3350, 25% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.73→47.317 Å / Num. obs: 67241 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 7.8
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 2 % / Num. unique obs: 3667 / CC1/2: 0.466 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0258refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→47.317 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.16 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2096 3192 4.918 %
Rwork0.1797 61706 -
all0.181 --
obs-64898 99.06 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.309 Å2
Baniso -1Baniso -2Baniso -3
1-1.106 Å20 Å20.937 Å2
2---0.05 Å2-0 Å2
3----1.071 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4971 0 124 285 5380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125215
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6497079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8295636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66121.44250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0415873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0511536
X-RAY DIFFRACTIONr_chiral_restr0.1070.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023950
X-RAY DIFFRACTIONr_nbd_refined0.2160.22523
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2322
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.211
X-RAY DIFFRACTIONr_mcbond_it1.9812.3412549
X-RAY DIFFRACTIONr_mcangle_it2.7553.4953179
X-RAY DIFFRACTIONr_scbond_it3.052.572666
X-RAY DIFFRACTIONr_scangle_it4.4073.7233899
X-RAY DIFFRACTIONr_lrange_it7.07932.6058074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.3351900.3224533X-RAY DIFFRACTION98.0079
1.795-1.8450.3321840.2954439X-RAY DIFFRACTION98.4245
1.845-1.8980.3241910.2624317X-RAY DIFFRACTION98.5355
1.898-1.9560.2622330.2424141X-RAY DIFFRACTION98.7359
1.956-2.0210.2682270.2224026X-RAY DIFFRACTION98.7233
2.021-2.0910.2381910.2073910X-RAY DIFFRACTION98.9862
2.091-2.170.2261920.1963808X-RAY DIFFRACTION99.0344
2.17-2.2590.2312280.1873619X-RAY DIFFRACTION99.1495
2.259-2.3590.2131670.1693546X-RAY DIFFRACTION99.3578
2.359-2.4740.2252230.1743281X-RAY DIFFRACTION99.4325
2.474-2.6080.212050.1683176X-RAY DIFFRACTION99.4704
2.608-2.7660.2171800.1653013X-RAY DIFFRACTION99.5635
2.766-2.9570.2121390.1742870X-RAY DIFFRACTION99.6688
2.957-3.1930.21400.1632656X-RAY DIFFRACTION99.7503
3.193-3.4980.1771240.1552443X-RAY DIFFRACTION99.8056
3.498-3.910.174910.1472258X-RAY DIFFRACTION99.6606
3.91-4.5130.13790.1351983X-RAY DIFFRACTION99.8064
4.513-5.5230.161110.1451648X-RAY DIFFRACTION99.7166
5.523-7.7940.19700.1931299X-RAY DIFFRACTION99.5636
7.794-47.3170.197270.166741X-RAY DIFFRACTION98.5879

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