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- PDB-5z75: Artificial L-threonine 3-dehydrogenase designed by ancestral sequ... -

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Basic information

Entry
Database: PDB / ID: 5z75
TitleArtificial L-threonine 3-dehydrogenase designed by ancestral sequence reconstruction.
ComponentsArtificial L-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / ancestral sequence reconstruction / L-threonine 3-dehydrogenase
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 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)151,93817
Polymers148,0394
Non-polymers3,89913
Water9,404522
1
A: Artificial L-threonine 3-dehydrogenase
B: Artificial L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1419
Polymers74,0202
Non-polymers2,1217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-63 kcal/mol
Surface area22520 Å2
MethodPISA
2
C: Artificial L-threonine 3-dehydrogenase
D: Artificial L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7978
Polymers74,0202
Non-polymers1,7776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-50 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.556, 112.694, 92.896
Angle α, β, γ (deg.)90.00, 93.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 30322 - 324
21BB1 - 30322 - 324
12AA1 - 30322 - 324
22CC1 - 30322 - 324
13AA1 - 30322 - 324
23DD1 - 30322 - 324
14BB1 - 30622 - 327
24CC1 - 30622 - 327
15BB1 - 30622 - 327
25DD1 - 30622 - 327
16CC1 - 30622 - 327
26DD1 - 30622 - 327

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Artificial L-threonine 3-dehydrogenase


Mass: 37009.844 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.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→92.7 Å / Num. obs: 73459 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 32.5
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 3652 / % possible all: 99.7

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Processing

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

3wmx


Resolution: 2.1→92.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.52 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23513 3612 4.9 %RANDOM
Rwork0.19278 ---
obs0.19491 69820 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.065 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.01 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→92.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9750 0 251 522 10523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910240
X-RAY DIFFRACTIONr_bond_other_d0.0040.029521
X-RAY DIFFRACTIONr_angle_refined_deg1.21.99113888
X-RAY DIFFRACTIONr_angle_other_deg1.055322114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6351220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90624.978456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.589151749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4161544
X-RAY DIFFRACTIONr_chiral_restr0.0950.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02111205
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022140
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_it3.9823.2794892
X-RAY DIFFRACTIONr_mcbond_other3.9823.2794891
X-RAY DIFFRACTIONr_mcangle_it5.5594.96108
X-RAY DIFFRACTIONr_mcangle_other5.5584.9016109
X-RAY DIFFRACTIONr_scbond_it5.0793.7985348
X-RAY DIFFRACTIONr_scbond_other5.0793.7975320
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3125.4727739
X-RAY DIFFRACTIONr_long_range_B_refined9.36526.87212135
X-RAY DIFFRACTIONr_long_range_B_other9.36526.86812127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A370460.11
12B370460.11
21A365920.11
22C365920.11
31A373300.1
32D373300.1
41B375460.11
42C375460.11
51B388780.09
52D388780.09
61C375960.11
62D375960.11
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 278 -
Rwork0.245 5045 -
obs--98.61 %

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