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- PDB-3a9w: Crystal structure of L-Threonine bound L-Threonine dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 3a9w
TitleCrystal structure of L-Threonine bound L-Threonine dehydrogenase (Y137F) from Hyperthermophilic Archaeon Thermoplasma volcanium
ComponentsNDP-sugar epimerase
KeywordsOXIDOREDUCTASE / L-Threonine dehydrogenase
Function / homology
Function and homology information


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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / THREONINE / NDP-sugar epimerase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionNov 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: NDP-sugar epimerase
B: NDP-sugar epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5458
Polymers71,7442
Non-polymers1,8016
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-45 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.203, 46.369, 89.751
Angle α, β, γ (deg.)90.00, 113.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35871.891 Da / Num. of mol.: 2 / Mutation: Y137F
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

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Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 50% MPD, 0.1M SODIUM CACODYLATE(PH6.4), 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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→82.479 Å / Num. obs: 48616 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.06 / Net I/σ(I): 15.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 10 / Rsym value: 0.269 / % possible all: 99.3

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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 ENTY 3A1N

3a1n


Resolution: 1.85→30.5 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2954500.56 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 4864 9.9 %RANDOM
Rwork0.1912 43329 --
obs0.1912 48190 99.1 %-
Solvent computationBsol: 57.609 Å2
Displacement parametersBiso max: 71.62 Å2 / Biso mean: 21.688 Å2 / Biso min: 6.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.458 Å2
2---0.108 Å20 Å2
3---0.098 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.85→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4982 0 120 247 5349
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d7.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.5142
X-RAY DIFFRACTIONc_scangle_it3.3532.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 743 10 %
Rwork0.228 6699 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4nad.param
X-RAY DIFFRACTION5MPD.param

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