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- PDB-7eps: Partial Consensus L-threonine 3-dehydrogenase (E-change) -

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Basic information

Entry
Database: PDB / ID: 7eps
TitlePartial Consensus L-threonine 3-dehydrogenase (E-change)
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / L-threonine 3-dehydrogenase / artificial protein
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / THREONINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsKozuka, K. / Nakano, S. / Asano, Y. / Ito, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K14391 Japan
Japan Society for the Promotion of Science (JSPS)17H06169 Japan
Japan Science and TechnologyJPMJPR20AB Japan
CitationJournal: Biochemistry / Year: 2021
Title: Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations.
Authors: Kozuka, K. / Nakano, S. / Asano, Y. / Ito, S.
History
DepositionApr 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,11814
Polymers147,2794
Non-polymers3,83910
Water10,341574
1
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9138
Polymers73,6392
Non-polymers2,2746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-27 kcal/mol
Surface area22480 Å2
MethodPISA
2
C: L-threonine 3-dehydrogenase
D: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2046
Polymers73,6392
Non-polymers1,5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-27 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.108, 180.932, 141.713
Angle α, β, γ (deg.)90.000, 90.007, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 6 - 315 / Label seq-ID: 26 - 335

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
221BB
332AA
442CC
553AA
663DD
774BB
884CC
995BB
10105DD
11116CC
12126DD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
L-threonine 3-dehydrogenase /


Mass: 36819.676 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)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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: Chemical
ChemComp-THR / THREONINE / Threonine


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% [w/v] PEG 3350, 0.2M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.4 Å / Num. obs: 878278 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.22 Å / Rmerge(I) obs: 0.57 / Num. unique obs: 18253 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMX
Resolution: 2.102→49.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.947 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.148
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2348 6302 5.021 %
Rwork0.2072 119215 -
all0.209 --
obs-125517 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.893 Å2
Baniso -1Baniso -2Baniso -3
1-2.362 Å2-0 Å20.103 Å2
2---0.899 Å20 Å2
3----1.463 Å2
Refinement stepCycle: LAST / Resolution: 2.102→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9460 0 256 574 10290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0139964
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179267
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.65113593
X-RAY DIFFRACTIONr_angle_other_deg1.4061.57221355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01251225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55722.288472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.502151520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7671558
X-RAY DIFFRACTIONr_chiral_restr0.0780.21340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211261
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022219
X-RAY DIFFRACTIONr_nbd_refined0.2130.21997
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.28724
X-RAY DIFFRACTIONr_nbtor_refined0.1690.24917
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2571
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1040.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5410.235
X-RAY DIFFRACTIONr_nbd_other0.4390.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.213
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0630.21
X-RAY DIFFRACTIONr_mcbond_it2.9593.1594930
X-RAY DIFFRACTIONr_mcbond_other2.9593.1594929
X-RAY DIFFRACTIONr_mcangle_it3.9664.7226145
X-RAY DIFFRACTIONr_mcangle_other3.9664.7226146
X-RAY DIFFRACTIONr_scbond_it3.4913.4885034
X-RAY DIFFRACTIONr_scbond_other3.4923.4885035
X-RAY DIFFRACTIONr_scangle_it5.0965.0847448
X-RAY DIFFRACTIONr_scangle_other5.0965.0847449
X-RAY DIFFRACTIONr_lrange_it6.82437.74711338
X-RAY DIFFRACTIONr_lrange_other6.82837.75111339
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.0510014
X-RAY DIFFRACTIONr_ncsr_local_group_20.0520.0510354
X-RAY DIFFRACTIONr_ncsr_local_group_30.0750.059980
X-RAY DIFFRACTIONr_ncsr_local_group_40.0790.059974
X-RAY DIFFRACTIONr_ncsr_local_group_50.0590.0510136
X-RAY DIFFRACTIONr_ncsr_local_group_60.0810.059945
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.073890.05009
12BX-RAY DIFFRACTIONLocal ncs0.073890.05009
23AX-RAY DIFFRACTIONLocal ncs0.051850.0501
24CX-RAY DIFFRACTIONLocal ncs0.051850.0501
35AX-RAY DIFFRACTIONLocal ncs0.075390.05008
36DX-RAY DIFFRACTIONLocal ncs0.075390.05008
47BX-RAY DIFFRACTIONLocal ncs0.079110.05008
48CX-RAY DIFFRACTIONLocal ncs0.079110.05008
59BX-RAY DIFFRACTIONLocal ncs0.058860.05009
510DX-RAY DIFFRACTIONLocal ncs0.058860.05009
611CX-RAY DIFFRACTIONLocal ncs0.080620.05008
612DX-RAY DIFFRACTIONLocal ncs0.080620.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.1570.2895250.2588664X-RAY DIFFRACTION99.599
2.157-2.2160.2654090.2368651X-RAY DIFFRACTION100
2.216-2.280.2734390.2318362X-RAY DIFFRACTION100
2.28-2.350.2414180.2158081X-RAY DIFFRACTION100
2.35-2.4270.2494070.2087850X-RAY DIFFRACTION100
2.427-2.5120.2524220.2087617X-RAY DIFFRACTION100
2.512-2.6070.243750.2027301X-RAY DIFFRACTION100
2.607-2.7130.2374050.1977092X-RAY DIFFRACTION100
2.713-2.8340.2223250.1956780X-RAY DIFFRACTION100
2.834-2.9720.2173550.2196477X-RAY DIFFRACTION100
2.972-3.1330.2623530.2316125X-RAY DIFFRACTION100
3.133-3.3230.2852770.2355872X-RAY DIFFRACTION100
3.323-3.5520.2483010.2335468X-RAY DIFFRACTION100
3.552-3.8370.2442400.2055130X-RAY DIFFRACTION100
3.837-4.2020.1992440.1724683X-RAY DIFFRACTION100
4.202-4.6980.1752410.1534259X-RAY DIFFRACTION100
4.698-5.4240.1692020.1653779X-RAY DIFFRACTION100
5.424-6.640.2061410.2163202X-RAY DIFFRACTION100
6.64-9.380.2591290.2112463X-RAY DIFFRACTION100
9.38-49.40.284940.2541359X-RAY DIFFRACTION99.3165

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