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- PDB-5y1d: Monomeric L-threonine 3-dehydrogenase from metagenome database (a... -

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Basic information

Entry
Database: PDB / ID: 5y1d
TitleMonomeric L-threonine 3-dehydrogenase from metagenome database (apo form)
ComponentsNAD dependent epimerase/dehydratase family
KeywordsOXIDOREDUCTASE / Dehydrogenase / NAD+ binding protein
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
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
B: NAD dependent epimerase/dehydratase family


Theoretical massNumber of molelcules
Total (without water)75,0852
Polymers75,0852
Non-polymers00
Water6,467359
1
A: NAD dependent epimerase/dehydratase family


Theoretical massNumber of molelcules
Total (without water)37,5421
Polymers37,5421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD dependent epimerase/dehydratase family


Theoretical massNumber of molelcules
Total (without water)37,5421
Polymers37,5421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.386, 49.319, 113.602
Angle α, β, γ (deg.)90.00, 89.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD dependent epimerase/dehydratase family


Mass: 37542.316 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2M Potassium formate

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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→113.6 Å / Num. obs: 46791 / % possible obs: 95.7 % / Redundancy: 5.1 % / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→1.93 Å / % possible all: 96.5

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Processing

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

3wmx


Resolution: 1.9→113.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.662 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23328 2345 5 %RANDOM
Rwork0.19008 ---
obs0.19225 44434 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.291 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.02 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→113.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 0 359 5317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195066
X-RAY DIFFRACTIONr_bond_other_d0.0010.024726
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9636854
X-RAY DIFFRACTIONr_angle_other_deg0.733310946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0585614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69425.317252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50915910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9331522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021110
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_it2.0231.5972462
X-RAY DIFFRACTIONr_mcbond_other2.0231.5962461
X-RAY DIFFRACTIONr_mcangle_it2.732.3863074
X-RAY DIFFRACTIONr_mcangle_other2.732.3873075
X-RAY DIFFRACTIONr_scbond_it3.2741.9452604
X-RAY DIFFRACTIONr_scbond_other3.2711.9442602
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8882.7793780
X-RAY DIFFRACTIONr_long_range_B_refined5.76913.4926114
X-RAY DIFFRACTIONr_long_range_B_other5.74313.3055980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.904→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 131 -
Rwork0.222 3019 -
obs--86.16 %

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