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- PDB-5k4y: Three-dimensional structure of L-threonine 3-dehydrogenase from T... -

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Basic information

Entry
Database: PDB / ID: 5k4y
TitleThree-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei refined to 1.77 angstroms
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Short-chain dehydrogenase / threonine / 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: 1.77 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 1.0Jan 17, 2018Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)219,09133
Polymers214,2556
Non-polymers4,83627
Water26,0861448
1
C: L-threonine 3-dehydrogenase
hetero molecules

A: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,98010
Polymers71,4182
Non-polymers1,5628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x+1/2,-y+5/2,-z1
2
B: L-threonine 3-dehydrogenase
hetero molecules

D: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,03912
Polymers71,4182
Non-polymers1,62010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475x-1/2,-y+5/2,-z1
3
E: L-threonine 3-dehydrogenase
hetero molecules

F: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,07211
Polymers71,4182
Non-polymers1,6549
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_676-x+1,-y+2,z+11
4
A: L-threonine 3-dehydrogenase
hetero molecules

C: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,98010
Polymers71,4182
Non-polymers1,5628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475x-1/2,-y+5/2,-z1
Buried area6050 Å2
ΔGint-83 kcal/mol
Surface area24780 Å2
MethodPISA
5
D: L-threonine 3-dehydrogenase
hetero molecules

B: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,03912
Polymers71,4182
Non-polymers1,62010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x+1/2,-y+5/2,-z1
Buried area6360 Å2
ΔGint-109 kcal/mol
Surface area24520 Å2
MethodPISA
6
F: L-threonine 3-dehydrogenase
hetero molecules

E: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,07211
Polymers71,4182
Non-polymers1,6549
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_674-x+1,-y+2,z-11
Buried area6350 Å2
ΔGint-82 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.451, 278.630, 56.270
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 ABCDEF

#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

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Non-polymers , 6 types, 1475 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1448 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M tri-sodium citrate, 25% w/v PEG 4K, 0.2M sodium acetate, NAD+ (10mM)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92001 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 1.77→40.12 Å / Num. obs: 203411 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.77-1.86.30.414199.9
9.72-40.126.50.037198.6

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Processing

Software
NameVersionClassification
Aimless0.1.26data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→39.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.129 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 10231 5 %RANDOM
Rwork0.1607 ---
obs0.1627 193067 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.03 Å2 / Biso mean: 19.218 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.77→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14998 0 308 1448 16754
Biso mean--13.37 25.84 -
Num. residues----1919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215871
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215135
X-RAY DIFFRACTIONr_angle_refined_deg1.9752.00821625
X-RAY DIFFRACTIONr_angle_other_deg0.9533.00234868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7851980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18223.873630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.545152743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9861594
X-RAY DIFFRACTIONr_chiral_restr0.130.22455
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02117516
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023318
X-RAY DIFFRACTIONr_mcbond_it1.8031.6967770
X-RAY DIFFRACTIONr_mcbond_other1.8011.6957763
X-RAY DIFFRACTIONr_mcangle_it2.5572.5339715
LS refinement shellResolution: 1.774→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 736 -
Rwork0.182 14203 -
all-14939 -
obs--99.93 %

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