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

ID or keywords:

Entry

Database: PDB / ID: 7eps

Title

Partial Consensus L-threonine 3-dehydrogenase (E-change)

Components

L-threonine 3-dehydrogenase

Keywords

OXIDOREDUCTASE / L-threonine 3-dehydrogenase / artificial protein

Function / homology

NICOTINAMIDE-ADENINE-DINUCLEOTIDE / THREONINE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.102 Å

Authors

Kozuka, K. / Nakano, S. / Asano, Y. / Ito, S.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	18K14391	Japan
Japan Society for the Promotion of Science (JSPS)	17H06169	Japan
Japan Science and Technology	JPMJPR20AB	Japan

Citation

Journal: 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

Deposition	Apr 27, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 11, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7eps.cif.gz	271 KB	Display	PDBx/mmCIF format
PDB format	pdb7eps.ent.gz	210 KB	Display	PDB format
PDBx/mmJSON format	7eps.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7eps_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	7eps_full_validation.pdf.gz	3.3 MB	Display
Data in XML	7eps_validation.xml.gz	51.2 KB	Display
Data in CIF	7eps_validation.cif.gz	72.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ep/7eps ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7eps	HTTPS FTP

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Related structure data

Related structure data	7eprC 3wmxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7eps-2 3wmx-1 3wmx-2 5z75-1 5upk-d 2wg3-2 3e66-d 3k1g-12 6bwl-1 3ajr-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: L-threonine 3-dehydrogenase

B: L-threonine 3-dehydrogenase

C: L-threonine 3-dehydrogenase

D: L-threonine 3-dehydrogenase

hetero molecules

151 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: L-threonine 3-dehydrogenase

B: L-threonine 3-dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
75.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: L-threonine 3-dehydrogenase

D: L-threonine 3-dehydrogenase

hetero molecules

defined by author&software
75.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

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-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	A	A
2	2	1	B	B
3	3	2	A	A
4	4	2	C	C
5	5	3	A	A
6	6	3	D	D
7	7	4	B	B
8	8	4	C	C
9	9	5	B	B
10	10	5	D	D
11	11	6	C	C
12	12	6	D	D

NCS ensembles :

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

#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 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 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 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 Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.75 Å³/Da / Density % sol: 67.18 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% [w/v] PEG 3350, 0.2M magnesium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→49.4 Å / Num. obs: 878278 / % possible obs: 100 % / Redundancy: 7 % / CC_1/2: 1 / R_merge(I) obs: 0.087 / Net I/σ(I): 15.5
Reflection shell	Resolution: 2.1→2.22 Å / R_merge(I) obs: 0.57 / Num. unique obs: 18253 / CC_1/2: 0.895

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WMX

3wmx

Resolution: 2.102→49.4 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.2348	6302	5.021 %
R_work	0.2072	119215	-
all	0.209	-	-
obs	-	125517	99.963 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 31.893 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.362 Å²	-0 Å²	0.103 Å²
2-	-	-0.899 Å²	0 Å²
3-	-	-	-1.463 Å²

Refinement step

Cycle: LAST / Resolution: 2.102→49.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9460	0	256	574	10290

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	9964
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	9267
X-RAY DIFFRACTION	r_angle_refined_deg	1.607	1.651	13593
X-RAY DIFFRACTION	r_angle_other_deg	1.406	1.572	21355
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.012	5	1225
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.557	22.288	472
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.502	15	1520
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.767	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1340
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	11261
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2219
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	1997
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	8724
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	4917
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	4632
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	571
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.104	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.541	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.439	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.186	0.2	13
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.063	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.959	3.159	4930
X-RAY DIFFRACTION	r_mcbond_other	2.959	3.159	4929
X-RAY DIFFRACTION	r_mcangle_it	3.966	4.722	6145
X-RAY DIFFRACTION	r_mcangle_other	3.966	4.722	6146
X-RAY DIFFRACTION	r_scbond_it	3.491	3.488	5034
X-RAY DIFFRACTION	r_scbond_other	3.492	3.488	5035
X-RAY DIFFRACTION	r_scangle_it	5.096	5.084	7448
X-RAY DIFFRACTION	r_scangle_other	5.096	5.084	7449
X-RAY DIFFRACTION	r_lrange_it	6.824	37.747	11338
X-RAY DIFFRACTION	r_lrange_other	6.828	37.751	11339
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.074	0.05	10014
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.052	0.05	10354
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.075	0.05	9980
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.079	0.05	9974
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.059	0.05	10136
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.081	0.05	9945

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07389	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07389	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05185	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.05185	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07539	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07539	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.07911	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.07911	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.05886	0.05009
5	10	D	X-RAY DIFFRACTION	Local ncs	0.05886	0.05009
6	11	C	X-RAY DIFFRACTION	Local ncs	0.08062	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.08062	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.102-2.157	0.289	525	0.258	8664	X-RAY DIFFRACTION	99.599
2.157-2.216	0.265	409	0.236	8651	X-RAY DIFFRACTION	100
2.216-2.28	0.273	439	0.231	8362	X-RAY DIFFRACTION	100
2.28-2.35	0.241	418	0.215	8081	X-RAY DIFFRACTION	100
2.35-2.427	0.249	407	0.208	7850	X-RAY DIFFRACTION	100
2.427-2.512	0.252	422	0.208	7617	X-RAY DIFFRACTION	100
2.512-2.607	0.24	375	0.202	7301	X-RAY DIFFRACTION	100
2.607-2.713	0.237	405	0.197	7092	X-RAY DIFFRACTION	100
2.713-2.834	0.222	325	0.195	6780	X-RAY DIFFRACTION	100
2.834-2.972	0.217	355	0.219	6477	X-RAY DIFFRACTION	100
2.972-3.133	0.262	353	0.231	6125	X-RAY DIFFRACTION	100
3.133-3.323	0.285	277	0.235	5872	X-RAY DIFFRACTION	100
3.323-3.552	0.248	301	0.233	5468	X-RAY DIFFRACTION	100
3.552-3.837	0.244	240	0.205	5130	X-RAY DIFFRACTION	100
3.837-4.202	0.199	244	0.172	4683	X-RAY DIFFRACTION	100
4.202-4.698	0.175	241	0.153	4259	X-RAY DIFFRACTION	100
4.698-5.424	0.169	202	0.165	3779	X-RAY DIFFRACTION	100
5.424-6.64	0.206	141	0.216	3202	X-RAY DIFFRACTION	100
6.64-9.38	0.259	129	0.211	2463	X-RAY DIFFRACTION	100
9.38-49.4	0.284	94	0.254	1359	X-RAY DIFFRACTION	99.3165

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