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- PDB-7cgv: Full consensus L-threonine 3-dehydrogenase, FcTDH-IIYM (NAD+ boun... -

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Basic information

Entry
Database: PDB / ID: 7cgv
TitleFull consensus L-threonine 3-dehydrogenase, FcTDH-IIYM (NAD+ bound form)
ComponentsArtificial L-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / L-Threonine 3-dehydrogenase / Artificial protein / Full consensus design
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsMotoyama, T. / Hiramatsu, N. / Asano, Y. / Nakano, S. / Ito, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H06169 Japan
Japan Society for the Promotion of Science (JSPS)18K14391 Japan
CitationJournal: Biochemistry / Year: 2020
Title: Protein Sequence Selection Method That Enables Full Consensus Design of Artificial l-Threonine 3-Dehydrogenases with Unique Enzymatic Properties.
Authors: Motoyama, T. / Hiramatsu, N. / Asano, Y. / Nakano, S. / Ito, S.
History
DepositionJul 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Artificial L-threonine 3-dehydrogenase
B: Artificial L-threonine 3-dehydrogenase
C: Artificial L-threonine 3-dehydrogenase
D: Artificial L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,3398
Polymers151,6854
Non-polymers2,6544
Water3,513195
1
A: Artificial L-threonine 3-dehydrogenase
B: Artificial L-threonine 3-dehydrogenase
hetero molecules

C: Artificial L-threonine 3-dehydrogenase
D: Artificial L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,3398
Polymers151,6854
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_446x-1,y-1,z+11
Buried area10700 Å2
ΔGint-55 kcal/mol
Surface area47440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.575, 77.513, 76.834
Angle α, β, γ (deg.)71.012, 75.129, 74.877
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Artificial L-threonine 3-dehydrogenase


Mass: 37921.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: L-threonine 3-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 2.5mM NAD+, 12% PEG 3350, 0.1M sodium acetate trihydrate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→36.41 Å / Num. obs: 48940 / % possible obs: 96.17 % / Redundancy: 3.4 % / Biso Wilson estimate: 43.67 Å2 / CC1/2: 0.985 / Net I/σ(I): 11.4
Reflection shellResolution: 2.38→2.47 Å / Num. unique obs: 4236 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMX

3wmx


Resolution: 2.38→36.41 Å / SU ML: 0.3694 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.1435
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 2253 4.61 %
Rwork0.2121 46656 -
obs0.2145 48909 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.16 Å2
Refinement stepCycle: LAST / Resolution: 2.38→36.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9682 0 176 195 10053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009610113
X-RAY DIFFRACTIONf_angle_d1.17613763
X-RAY DIFFRACTIONf_chiral_restr0.0581506
X-RAY DIFFRACTIONf_plane_restr0.00671754
X-RAY DIFFRACTIONf_dihedral_angle_d16.32461495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.37451320.28932252X-RAY DIFFRACTION74.92
2.44-2.490.29121420.26062930X-RAY DIFFRACTION96.18
2.49-2.550.31111310.26062951X-RAY DIFFRACTION96.83
2.55-2.620.33271610.25132900X-RAY DIFFRACTION97.21
2.62-2.70.29911690.2412923X-RAY DIFFRACTION97.14
2.7-2.790.31351330.24722985X-RAY DIFFRACTION97.29
2.79-2.890.36441260.25312969X-RAY DIFFRACTION98.19
2.89-30.31051170.2383001X-RAY DIFFRACTION98.42
3-3.140.31031550.24312964X-RAY DIFFRACTION98.52
3.14-3.310.26161180.23213044X-RAY DIFFRACTION98.72
3.31-3.510.32091440.23782995X-RAY DIFFRACTION98.84
3.51-3.780.32191080.25882745X-RAY DIFFRACTION90.63
3.78-4.160.23031640.18932992X-RAY DIFFRACTION99.09
4.16-4.760.21341490.16333038X-RAY DIFFRACTION99.25
4.76-60.20171460.173005X-RAY DIFFRACTION99.37
6-36.410.21321580.17162962X-RAY DIFFRACTION98.42

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