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- PDB-5z76: Artificial L-threonine 3-dehydrogenase designed by full consensus... -

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Basic information

Entry
Database: PDB / ID: 5z76
TitleArtificial L-threonine 3-dehydrogenase designed by full consensus design
ComponentsArtificial L-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / L-threonine 3-dehydrogenase / full consensus design
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNakano, S. / Motoyama, T. / Miyashita, Y. / Ishizuka, Y. / Matsuo, N. / Tokiwa, H. / Shinoda, S. / Asano, Y. / Ito, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS16K18688 Japan
CitationJournal: Biochemistry / Year: 2018
Title: Benchmark Analysis of Native and Artificial NAD+-Dependent Enzymes Generated by a Sequence-Based Design Method with or without Phylogenetic Data.
Authors: Nakano, S. / Motoyama, T. / Miyashita, Y. / Ishizuka, Y. / Matsuo, N. / Tokiwa, H. / Shinoda, S. / Asano, Y. / Ito, S.
History
DepositionJan 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,6374
Polymers151,6374
Non-polymers00
Water00
1
A: Artificial L-threonine 3-dehydrogenase
C: Artificial L-threonine 3-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)75,8182
Polymers75,8182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-17 kcal/mol
Surface area25710 Å2
MethodPISA
2
B: Artificial L-threonine 3-dehydrogenase
D: Artificial L-threonine 3-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)75,8182
Polymers75,8182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-14 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.460, 93.540, 176.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Artificial L-threonine 3-dehydrogenase


Mass: 37909.156 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

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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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→52.9 Å / Num. obs: 38858 / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 15.6
Reflection shellResolution: 2.8→2.93 Å / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMX

3wmx


Resolution: 2.8→52.884 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1895 4.89 %RANDOM
Rwork0.2151 ---
obs0.2156 38784 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→52.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9449 0 0 0 9449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079665
X-RAY DIFFRACTIONf_angle_d1.12813088
X-RAY DIFFRACTIONf_dihedral_angle_d14.7523607
X-RAY DIFFRACTIONf_chiral_restr0.0641432
X-RAY DIFFRACTIONf_plane_restr0.0051665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.87010.34431330.34022602X-RAY DIFFRACTION100
2.8701-2.94760.30221050.28612610X-RAY DIFFRACTION100
2.9476-3.03440.27131290.2712610X-RAY DIFFRACTION100
3.0344-3.13230.26891280.26372591X-RAY DIFFRACTION100
3.1323-3.24420.28061490.25782599X-RAY DIFFRACTION100
3.2442-3.37410.23791440.24312594X-RAY DIFFRACTION100
3.3741-3.52760.25581520.23372572X-RAY DIFFRACTION100
3.5276-3.71360.21751350.21092619X-RAY DIFFRACTION100
3.7136-3.94620.22351240.20242648X-RAY DIFFRACTION100
3.9462-4.25070.21091410.19112639X-RAY DIFFRACTION100
4.2507-4.67830.16651360.17272635X-RAY DIFFRACTION100
4.6783-5.35470.17921290.17952682X-RAY DIFFRACTION100
5.3547-6.74410.2261570.20622658X-RAY DIFFRACTION100
6.7441-52.89380.21341330.20812830X-RAY DIFFRACTION100

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