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- PDB-5k4q: Three-dimensional structure of L-threonine 3-dehydrogenase from T... -

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Basic information

Entry
Database: PDB / ID: 5k4q
TitleThree-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ refined to 2.3 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-threonine 3-dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 21, 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
B: L-threonine 3-dehydrogenase
C: L-threonine 3-dehydrogenase
D: L-threonine 3-dehydrogenase
E: L-threonine 3-dehydrogenase
F: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,26823
Polymers214,2556
Non-polymers5,01317
Water16,718928
1
A: L-threonine 3-dehydrogenase
hetero molecules

C: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0257
Polymers71,4182
Non-polymers1,6075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
MethodPISA
2
D: L-threonine 3-dehydrogenase
hetero molecules

B: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2189
Polymers71,4182
Non-polymers1,7997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
MethodPISA
3
E: L-threonine 3-dehydrogenase
hetero molecules

F: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0257
Polymers71,4182
Non-polymers1,6075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,-y,z+11
MethodPISA
4
C: L-threonine 3-dehydrogenase
hetero molecules

A: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0257
Polymers71,4182
Non-polymers1,6075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area5640 Å2
ΔGint-39 kcal/mol
Surface area24950 Å2
MethodPISA
5
B: L-threonine 3-dehydrogenase
hetero molecules

D: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2189
Polymers71,4182
Non-polymers1,7997
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area5960 Å2
ΔGint-57 kcal/mol
Surface area24950 Å2
MethodPISA
6
F: L-threonine 3-dehydrogenase
hetero molecules

E: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0257
Polymers71,4182
Non-polymers1,6075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,-y,z-11
Buried area5580 Å2
ΔGint-37 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.630, 277.720, 56.000
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.: 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
#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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium sulphate, 0.1M Tris, 30% w/v PEG 4K, pH 8.5, NAD+ (0.09mM)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Feb 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.3→48.143 Å / Num. obs: 93173 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.424.60.2762.7195.3
2.42-2.576.50.2433.1199.7
2.57-2.757.40.2073.51100
2.75-2.977.40.1664.21100
2.97-3.257.40.135.11100
3.25-3.647.30.1065.91100
3.64-4.27.10.0956.21100
4.2-5.146.90.0896.31100
5.14-7.276.60.0916199.8
7.27-48.4086.10.085.2199.4

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.143 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.84 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 4653 5 %RANDOM
Rwork0.174 ---
obs0.1775 88435 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.91 Å2 / Biso mean: 21.09 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.05 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.3→48.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14974 0 325 928 16227
Biso mean--25.08 21.74 -
Num. residues----1916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215682
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214931
X-RAY DIFFRACTIONr_angle_refined_deg1.7132.00821329
X-RAY DIFFRACTIONr_angle_other_deg0.8743.00234361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95851918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44323.893619
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.369152684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1531590
X-RAY DIFFRACTIONr_chiral_restr0.0950.22429
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023266
X-RAY DIFFRACTIONr_mcbond_it1.5922.1977672
X-RAY DIFFRACTIONr_mcbond_other1.592.1967671
X-RAY DIFFRACTIONr_mcangle_it2.5543.2859584
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 295 -
Rwork0.216 6058 -
all-6353 -
obs--93 %

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