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- PDB-5y1e: monomeric L-threonine 3-dehydrogenase from metagenome database (L... -

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Basic information

Entry
Database: PDB / ID: 5y1e
Titlemonomeric L-threonine 3-dehydrogenase from metagenome database (L-Ser and NAD+ bound form)
ComponentsNAD dependent epimerase/dehydratase family
KeywordsOXIDOREDUCTASE / dehydrogenase / NAD+ / L-Ser
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 / SERINE / NAD dependent epimerase/dehydratase family
Similarity search - Component
Biological speciesuncultured archaeon MedDCM-OCT-S05-C57 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMotoyama, T. / Nakano, S. / Yamamoto, Y. / Tokiwa, H. / Asano, Y. / Ito, S.
CitationJournal: Biochemistry / Year: 2017
Title: Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase.
Authors: Motoyama, T. / Nakano, S. / Yamamoto, Y. / Tokiwa, H. / Asano, Y. / Ito, S.
History
DepositionJul 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD dependent epimerase/dehydratase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3113
Polymers37,5421
Non-polymers7692
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area13030 Å2
Unit cell
Length a, b, c (Å)112.594, 50.857, 55.252
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NAD dependent epimerase/dehydratase family


Mass: 37542.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured archaeon MedDCM-OCT-S05-C57 (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: D6PBM7
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2M Sodium fluoride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→54.2 Å / Num. obs: 23337 / % possible obs: 98.7 % / Redundancy: 6.6 % / Net I/σ(I): 17.2
Reflection shellResolution: 1.9→1.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMX

3wmx


Resolution: 1.9→54.22 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.25 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1150 4.9 %RANDOM
Rwork0.15822 ---
obs0.16022 22187 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.277 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.01 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→54.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 51 156 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192587
X-RAY DIFFRACTIONr_bond_other_d0.0010.022391
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9863507
X-RAY DIFFRACTIONr_angle_other_deg0.81135539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2095307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02425.317126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2615456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0691511
X-RAY DIFFRACTIONr_chiral_restr0.2110.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
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_it2.3081.6451234
X-RAY DIFFRACTIONr_mcbond_other2.2921.6441233
X-RAY DIFFRACTIONr_mcangle_it3.092.451539
X-RAY DIFFRACTIONr_mcangle_other3.0892.4521540
X-RAY DIFFRACTIONr_scbond_it4.0492.0611353
X-RAY DIFFRACTIONr_scbond_other4.0142.0611352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9282.9161969
X-RAY DIFFRACTIONr_long_range_B_refined6.84913.8983075
X-RAY DIFFRACTIONr_long_range_B_other6.85413.8013038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 80 -
Rwork0.209 1458 -
obs--87.99 %

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