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- PDB-3a1n: Crystal structure of L-Threonine dehydrogenase from Hyperthermoph... -

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Basic information

Entry
Database: PDB / ID: 3a1n
TitleCrystal structure of L-Threonine dehydrogenase from Hyperthermophilic Archaeon Thermoplasma volcanium
ComponentsNDP-sugar epimerase
KeywordsOXIDOREDUCTASE / L-threonine dehydrogenase
Function / homology
Function and homology information


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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NDP-sugar epimerase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsYoneda, K. / Sakuraba, H. / Ohshima, T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Binary and Ternary Complexes of Archaeal UDP-galactose 4-Epimerase-like L-Threonine Dehydrogenase from Thermoplasma volcanium.
Authors: Yoneda, K. / Sakuraba, H. / Araki, T. / Ohshima, T.
History
DepositionApr 18, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: NDP-sugar epimerase
B: NDP-sugar epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1034
Polymers71,7762
Non-polymers1,3272
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-32 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.759, 45.618, 89.036
Angle α, β, γ (deg.)90.00, 113.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

#1: Protein NDP-sugar epimerase / L-threonine dehydrogenase


Mass: 35887.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q97BK3, L-threonine 3-dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.95 Å3/Da / Density % sol: 36.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 48% MPD, 0.1M Cacodylate (pH6.8), 5% PEG 8000, 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: Mar 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→81.9 Å / Num. obs: 33993 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 36.8
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 7.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YY7

2yy7


Resolution: 2.07→30.34 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3073719.82 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3382 10 %RANDOM
Rwork0.215 ---
obs-33896 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9906 Å2 / ksol: 0.32957 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å21.09 Å2
2---0.22 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.07→30.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 88 258 5330
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.5211.5
X-RAY DIFFRACTIONc_mcangle_it2.5142
X-RAY DIFFRACTIONc_scbond_it4.3333
X-RAY DIFFRACTIONc_scangle_it6.544.5
LS refinement shellResolution: 2.07→2.2 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 541 9.9 %
Rwork0.261 4912 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4nad.paramnad.top

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