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- PDB-5lc1: L-threonine dehydrogenase from Trypanosoma brucei with NAD and th... -

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Basic information

Entry
Database: PDB / ID: 5lc1
TitleL-threonine dehydrogenase from Trypanosoma brucei with NAD and the inhibitor pyruvate bound.
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / holo-enzyme / Rossman fold
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 / BETA-MERCAPTOETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRUVIC ACID / L-threonine 3-dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsErskine, P.T. / Adjogatse, E. / Wood, S.P. / 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
DepositionJun 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Apr 3, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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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)220,06429
Polymers215,0846
Non-polymers4,98023
Water35,3451962
1
C: L-threonine 3-dehydrogenase
hetero molecules

A: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,38110
Polymers71,6952
Non-polymers1,6868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
MethodPISA
2
A: L-threonine 3-dehydrogenase
hetero molecules

C: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,38110
Polymers71,6952
Non-polymers1,6868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area6150 Å2
ΔGint-47 kcal/mol
Surface area23910 Å2
MethodPISA
3
D: L-threonine 3-dehydrogenase
hetero molecules

B: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,38110
Polymers71,6952
Non-polymers1,6868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
MethodPISA
4
B: L-threonine 3-dehydrogenase
hetero molecules

D: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,38110
Polymers71,6952
Non-polymers1,6868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area6110 Å2
ΔGint-46 kcal/mol
Surface area24360 Å2
MethodPISA
5
F: L-threonine 3-dehydrogenase
hetero molecules

E: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3039
Polymers71,6952
Non-polymers1,6087
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,-y,z-11
MethodPISA
6
E: L-threonine 3-dehydrogenase
hetero molecules

F: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3039
Polymers71,6952
Non-polymers1,6087
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,-y,z+11
Buried area5970 Å2
ΔGint-46 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.040, 276.490, 55.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
L-threonine 3-dehydrogenase


Mass: 35847.305 Da / Num. of mol.: 6
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

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Non-polymers , 6 types, 1985 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-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1962 / 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: 45.1 %
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, 1 mM NAD(+), 30 mM pyruvate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.074 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 2.1→95.5 Å / Num. obs: 117204 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.2 / % possible all: 81.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
REFMAC5.8.0151refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9A

5l9a


Resolution: 2.1→95.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.668 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.176
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Note that the R-free set was chosen in thin resolution shells and hence the outer shell (Shell 1, below) did not contain any free-set ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Note that the R-free set was chosen in thin resolution shells and hence the outer shell (Shell 1, below) did not contain any free-set reflections. The R-free and N(R-free) given below relate the highest resolution shell which contained free-set reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.20763 5563 4.8 %RANDOM
Rwork0.14654 ---
obs0.14952 111527 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.76 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 2.1→95.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15010 0 326 1962 17298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01915737
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214971
X-RAY DIFFRACTIONr_angle_refined_deg1.7942.00521374
X-RAY DIFFRACTIONr_angle_other_deg1.035334610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87451922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18823.891622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.461152693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6051590
X-RAY DIFFRACTIONr_chiral_restr0.1080.22409
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117295
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023341
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_it1.7531.9337694
X-RAY DIFFRACTIONr_mcbond_other1.7521.9327693
X-RAY DIFFRACTIONr_mcangle_it2.6742.8849609
X-RAY DIFFRACTIONr_mcangle_other2.6752.8859610
X-RAY DIFFRACTIONr_scbond_it2.9862.2818043
X-RAY DIFFRACTIONr_scbond_other2.9862.288042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6013.26811764
X-RAY DIFFRACTIONr_long_range_B_refined7.48925.24319191
X-RAY DIFFRACTIONr_long_range_B_other7.12424.08218523
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å
RfactorNum. reflection% reflection
Rfree0.24 603 -
Rwork0.214 6960 -
obs--79 %

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