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- PDB-2yy7: Crystal structure of thermolabile L-threonine dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 2yy7
TitleCrystal structure of thermolabile L-threonine dehydrogenase from Flavobacterium frigidimaris KUC-1
ComponentsL-threonine dehydrogenaseL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / L-threonine dehydrogenase / thermolabile / Flavobacterium frigidimaris KUC-1
Function / homology
Function and homology information


catalytic activity / 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 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / L-threonine dehydrogenase
Similarity search - Component
Biological speciesFlavobacterium frigidimaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.061 Å
AuthorsYoneda, K. / Sakuraba, H. / Oikawa, T. / Muraoka, I. / Ohshima, T.
CitationJournal: Febs J. / Year: 2010
Title: Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily
Authors: Yoneda, K. / Sakuraba, H. / Muraoka, I. / Oikawa, T. / Ohshima, T.
History
DepositionApr 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-threonine dehydrogenase
B: L-threonine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,28612
Polymers70,9032
Non-polymers3,38310
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-25.5 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.029, 88.142, 123.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe ThrDH reported tetrameric enzyme in solution (Kazuoka et al.) and we checked the enzyme is dimeric structure in the crystal.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L-threonine dehydrogenase / L-threonine 3-dehydrogenase


Mass: 35451.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Flavobacterium frigidimaris (bacteria) / Strain: KUC-1 / References: UniProt: Q8KZM4, L-threonine 3-dehydrogenase

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Non-polymers , 5 types, 388 molecules

#2: Chemical
ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O9
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 32% PEG 600, 5% PEG 1000, 10% glycerol, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.061→88.045 Å / Num. obs: 44410 / Biso Wilson estimate: 17.1 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.061→46.474 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.203 -RANDOM
Rwork0.195 --
obs-44408 -
Refinement stepCycle: LAST / Resolution: 2.061→46.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 224 378 5586

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