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- PDB-3wmx: GalE-like L-Threonine dehydrogenase from Cupriavidus necator (hol... -

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Basic information

Entry
Database: PDB / ID: 3wmx
TitleGalE-like L-Threonine dehydrogenase from Cupriavidus necator (holo form)
ComponentsNAD dependent epimerase/dehydratase
KeywordsOXIDOREDUCTASE / extended short-chain dehydrogenase/reductase superfamily / Rossmann Fold / dehydrogenase / NAD+ binding
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases / L-threonine 3-dehydrogenase activity / threonine catabolic process / isomerase activity / nucleotide binding / metal ion 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 / L-threonine 3-dehydrogenase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNakano, S. / Okazaki, S. / Tokiwa, H. / Asano, Y.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Binding of NAD+ and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase
Authors: Nakano, S. / Okazaki, S. / Tokiwa, H. / Asano, Y.
History
DepositionNov 29, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 8, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: NAD dependent epimerase/dehydratase
B: NAD dependent epimerase/dehydratase
C: NAD dependent epimerase/dehydratase
D: NAD dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,39110
Polymers155,4994
Non-polymers2,8926
Water1,20767
1
A: NAD dependent epimerase/dehydratase
C: NAD dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1965
Polymers77,7502
Non-polymers1,4463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-26 kcal/mol
Surface area22800 Å2
MethodPISA
2
B: NAD dependent epimerase/dehydratase
D: NAD dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1965
Polymers77,7502
Non-polymers1,4463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-25 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.598, 88.109, 113.597
Angle α, β, γ (deg.)90.00, 105.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA6 - 31226 - 332
21LEULEUBB6 - 31226 - 332
12LEULEUAA6 - 31226 - 332
22LEULEUCC6 - 31226 - 332
13LEULEUAA6 - 31226 - 332
23LEULEUDD6 - 31226 - 332
14LYSLYSBB6 - 31326 - 333
24LYSLYSCC6 - 31326 - 333
15LEULEUBB6 - 31226 - 332
25LEULEUDD6 - 31226 - 332
16LEULEUCC6 - 31226 - 332
26LEULEUDD6 - 31226 - 332

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
NAD dependent epimerase/dehydratase


Mass: 38874.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: H16_B0820, h16_B0820 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q0K312, Oxidoreductases
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20%(w/v) PEG3350, 0.2M potassium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→40.9 Å / Num. obs: 60238 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A4V

3a4v


Resolution: 2.5→40.87 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.716 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23901 2997 5 %RANDOM
Rwork0.20409 ---
obs0.20582 57476 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9479 0 192 67 9738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199924
X-RAY DIFFRACTIONr_bond_other_d0.0030.029239
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.96913560
X-RAY DIFFRACTIONr_angle_other_deg0.877321231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08851225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38223.714420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.104151522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8551564
X-RAY DIFFRACTIONr_chiral_restr0.0660.21499
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111204
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022272
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A185230.1
12B185230.1
21A183570.12
22C183570.12
31A179910.13
32D179910.13
41B183900.13
42C183900.13
51B179840.14
52D179840.14
61C179710.13
62D179710.13
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 227 -
Rwork0.295 4223 -
obs--100 %

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