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- PDB-5k50: Three-dimensional structure of L-threonine 3-dehydrogenase from T... -

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Basic information

Entry
Database: PDB / ID: 5k50
TitleThree-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ and L-allo-threonine refined to 2.23 angstroms
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Short-chain dehydrogenase / threonine / holo / ligand-bound
Function / homology
Function and homology information


L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / L-threonine catabolic process / nucleotide binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ALLO-THREONINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-threonine 3-dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsAdjogatse, E.A. / Erskine, P.T. / Cooper, J.B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations.
Authors: Adjogatse, E. / Erskine, P. / Wells, S.A. / Kelly, J.M. / Wilden, J.D. / Chan, A.W.E. / Selwood, D. / Coker, A. / Wood, S. / Cooper, J.B.
History
DepositionMay 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: L-threonine 3-dehydrogenase
C: L-threonine 3-dehydrogenase
E: L-threonine 3-dehydrogenase
G: L-threonine 3-dehydrogenase
I: L-threonine 3-dehydrogenase
J: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,66026
Polymers213,4686
Non-polymers5,19220
Water7,927440
1
I: L-threonine 3-dehydrogenase
hetero molecules

J: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9109
Polymers71,1562
Non-polymers1,7547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,-y,z+11
2
A: L-threonine 3-dehydrogenase
E: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8188
Polymers71,1562
Non-polymers1,6626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-35 kcal/mol
Surface area24310 Å2
MethodPISA
3
C: L-threonine 3-dehydrogenase
G: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9319
Polymers71,1562
Non-polymers1,7757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-30 kcal/mol
Surface area24370 Å2
MethodPISA
4
J: L-threonine 3-dehydrogenase
hetero molecules

I: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9109
Polymers71,1562
Non-polymers1,7547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,-y,z-11
Buried area6210 Å2
ΔGint-33 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.030, 273.060, 55.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 6 molecules ACEGIJ

#1: Protein
L-threonine 3-dehydrogenase


Mass: 35577.965 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7YW97, L-threonine 3-dehydrogenase

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Non-polymers , 5 types, 460 molecules

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


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ALO / ALLO-THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.23 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M tri-sodium citrate, 30% w/v PEG 4K, 0.2M ammonium acetate, NAD+ (10mM), L-allo-threonine (30mM)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.26→31.09 Å / Num. obs: 154520 / % possible obs: 90.4 % / Redundancy: 1.9 % / CC1/2: 0.862 / Rmerge(I) obs: 0.151 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.26-2.341.90.403192.5
12.6-28.820.203191.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Aimless0.1.26data scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→31.09 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / SU B: 8.565 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 4815 5 %RANDOM
Rwork0.2073 ---
obs0.211 91289 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.74 Å2 / Biso mean: 33.758 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.26→31.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14958 0 344 440 15742
Biso mean--27.66 30.04 -
Num. residues----1914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215692
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214949
X-RAY DIFFRACTIONr_angle_refined_deg1.6492.00821329
X-RAY DIFFRACTIONr_angle_other_deg0.8623.00234390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50751916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37523.883618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.765152667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8961590
X-RAY DIFFRACTIONr_chiral_restr0.0890.22430
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023265
X-RAY DIFFRACTIONr_mcbond_it2.1863.2867690
X-RAY DIFFRACTIONr_mcbond_other2.1863.2857685
X-RAY DIFFRACTIONr_mcangle_it3.3874.9179594
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 341 -
Rwork0.26 6665 -
all-7006 -
obs--99.86 %

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