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- PDB-5y1f: Monomeric L-threonine 3-dehydrogenase from metagenome database (N... -

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Basic information

Entry
Database: PDB / ID: 5y1f
TitleMonomeric L-threonine 3-dehydrogenase from metagenome database (NAD+ bound form)
ComponentsNAD dependent epimerase/dehydratase family
KeywordsOXIDOREDUCTASE / dehydrogenase / NAD+
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 / NAD dependent epimerase/dehydratase family
Similarity search - Component
Biological speciesuncultured archaeon MedDCM-OCT-S05-C57 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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)38,2062
Polymers37,5421
Non-polymers6631
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-6 kcal/mol
Surface area13180 Å2
Unit cell
Length a, b, c (Å)113.494, 48.927, 56.364
Angle α, β, γ (deg.)90.00, 104.71, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
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: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→54.9 Å / Num. obs: 75876 / % possible obs: 91.5 % / Redundancy: 6.3 % / Net I/σ(I): 28.9
Reflection shellResolution: 1.25→1.28 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: 1.25→54.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.656 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18055 3743 4.9 %RANDOM
Rwork0.15709 ---
obs0.15827 72123 91.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.098 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.25→54.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 44 426 2969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192695
X-RAY DIFFRACTIONr_bond_other_d0.0010.022487
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9843667
X-RAY DIFFRACTIONr_angle_other_deg0.80235774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02625.42131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95915481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6391511
X-RAY DIFFRACTIONr_chiral_restr0.2710.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213077
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02599
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_it1.3591.1031293
X-RAY DIFFRACTIONr_mcbond_other1.3491.1011292
X-RAY DIFFRACTIONr_mcangle_it1.8921.6581632
X-RAY DIFFRACTIONr_mcangle_other1.8931.661633
X-RAY DIFFRACTIONr_scbond_it3.2041.411402
X-RAY DIFFRACTIONr_scbond_other3.2031.4091403
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6051.9932036
X-RAY DIFFRACTIONr_long_range_B_refined6.58511.3213667
X-RAY DIFFRACTIONr_long_range_B_other6.24910.183368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.248→1.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 320 -
Rwork0.218 5681 -
obs--98.02 %

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