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- PDB-5l9a: L-threonine dehydrogenase from trypanosoma brucei. -

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Basic information

Entry
Database: PDB / ID: 5l9a
TitleL-threonine dehydrogenase from trypanosoma brucei.
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Apo-enzyme / Rossmann fold / dehydrogenase
Function / homology
Function and homology information


L-threonine 3-dehydrogenase / L-threonine 3-dehydrogenase activity / 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 / L-threonine 3-dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsErskine, P.T. / Cooper, J.B. / Adjogatse, E. / Kelly, J. / Wood, S.P.
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
DepositionJun 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: 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 / _citation_author.name
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 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8134
Polymers71,6952
Non-polymers1182
Water24,0501335
1
A: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9062
Polymers35,8471
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9062
Polymers35,8471
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.985, 57.722, 70.074
Angle α, β, γ (deg.)72.46, 70.38, 73.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein L-threonine 3-dehydrogenase


Mass: 35847.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7YW97, L-threonine 3-dehydrogenase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1335 / 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: 2.2 Å3/Da / Density % sol: 44.2 % / Description: Thin plates.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 20 % w/v PEG 10K, TDH 2.0 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.45→53.82 Å / Num. obs: 109054 / % possible obs: 95 % / Redundancy: 3.8 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.4
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.7 / % possible all: 82.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yy7

2yy7


Resolution: 1.45→46.82 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.266 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15643 5491 5 %RANDOM
Rwork0.09969 ---
obs0.10254 103550 95.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.591 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.03 Å20.01 Å2
2---0 Å20.02 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.45→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5011 0 8 1335 6354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195339
X-RAY DIFFRACTIONr_bond_other_d0.0050.025106
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9827275
X-RAY DIFFRACTIONr_angle_other_deg1.325311828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63324.018219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76915943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.771532
X-RAY DIFFRACTIONr_chiral_restr0.1380.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216062
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021144
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_it1.5251.092676
X-RAY DIFFRACTIONr_mcbond_other1.4911.0882673
X-RAY DIFFRACTIONr_mcangle_it1.8371.6423378
X-RAY DIFFRACTIONr_mcangle_other1.8371.6433379
X-RAY DIFFRACTIONr_scbond_it3.2861.5032663
X-RAY DIFFRACTIONr_scbond_other3.2861.5042664
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.82.0853897
X-RAY DIFFRACTIONr_long_range_B_refined5.31313.4577685
X-RAY DIFFRACTIONr_long_range_B_other4.11510.746662
X-RAY DIFFRACTIONr_rigid_bond_restr4.414310445
X-RAY DIFFRACTIONr_sphericity_free40.1775333
X-RAY DIFFRACTIONr_sphericity_bonded11.902511313
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 265 -
Rwork0.216 5817 -
obs--71.23 %

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