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- PDB-5k4u: Three-dimensional structure of L-threonine 3-dehydrogenase from T... -

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Basic information

Entry
Database: PDB / ID: 5k4u
TitleThree-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei showing different active site loop conformations between dimer subunits, refined to 1.9 angstroms
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase / ligand-bound / holo
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-threonine 3-dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAdjogatse, E.K. / Cooper, J.B. / Erskine, P.T.
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,50114
Polymers71,4182
Non-polymers2,08312
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-32 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.074, 133.095, 55.606
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein L-threonine 3-dehydrogenase


Mass: 35709.160 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
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 sodium acetate, NAD+ (8.5mM)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.79→29.29 Å / Num. obs: 61881 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.79-1.893.30.46197.5
5.68-29.293.20.026196.9

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.027 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 2679 5.1 %RANDOM
Rwork0.1716 ---
obs0.1742 49596 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.08 Å2 / Biso mean: 23.973 Å2 / Biso min: 9.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å20 Å2
2--0.16 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.9→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5002 0 138 228 5368
Biso mean--24.5 28.5 -
Num. residues----640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.025250
X-RAY DIFFRACTIONr_bond_other_d0.0010.025007
X-RAY DIFFRACTIONr_angle_refined_deg1.942.0127128
X-RAY DIFFRACTIONr_angle_other_deg0.9293.00211518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8045638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42823.883206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59615894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8081530
X-RAY DIFFRACTIONr_chiral_restr0.120.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
X-RAY DIFFRACTIONr_mcbond_it2.0392.1922563
X-RAY DIFFRACTIONr_mcbond_other2.0272.1872557
X-RAY DIFFRACTIONr_mcangle_it2.8423.2713194
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 204 -
Rwork0.186 3584 -
all-3788 -
obs--97.55 %

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