PDB-7epr: Partial Consensus L-threonine 3-dehydrogenase (C-Change)

ID or keywords:

Entry

Database: PDB / ID: 7epr

Title

Partial Consensus L-threonine 3-dehydrogenase (C-Change)

Components

L-threonine 3-dehydrogenase

Keywords

OXIDOREDUCTASE /

L-threonine 3-dehydrogenase /

artificial protein

Function / homology

NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 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	7epr.cif.gz	262.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7epr.ent.gz	203.9 KB	Display	PDB format
PDBx/mmJSON format	7epr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ep/7epr ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7epr	HTTPS FTP

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Related structure data

Related structure data	7epsC 3wmxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3wmx-2 5z75-1 5z75-2 3a4v-d 7eps-2 4hr5-1 7epr-2 5vg6-3 3k1g-12 5dcs-1 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

152 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
75.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	149.019, 58.474, 138.130
Angle α, β, γ (deg.)	90.000, 92.234, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-577- HOH

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: LYS / Beg label comp-ID: LYS

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	A	A	5 - 314	25 - 334
2	2	1	ALA	ALA	B	B	5 - 314	25 - 334
3	3	2	ALA	ALA	A	A	5 - 314	25 - 334
4	4	2	ALA	ALA	C	C	5 - 314	25 - 334
5	5	3	LEU	LEU	A	A	7 - 312	27 - 332
6	6	3	LEU	LEU	D	D	7 - 312	27 - 332
7	7	4	ALA	ALA	B	B	5 - 314	25 - 334
8	8	4	ALA	ALA	C	C	5 - 314	25 - 334
9	9	5	LEU	LEU	B	B	7 - 312	27 - 332
10	10	5	LEU	LEU	D	D	7 - 312	27 - 332
11	11	6	LEU	LEU	C	C	7 - 312	27 - 332
12	12	6	LEU	LEU	D	D	7 - 312	27 - 332

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: 37286.289 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: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.02 Å³/Da / Density % sol: 38.99 %
Crystal grow	Temperature: 275 K / Method: vapor diffusion, sitting drop Details: 20% [w/v] PEG 3350, 0.2M sodium phosphate monobasic monohydrate

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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: Dec 6, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→46 Å / Num. obs: 412432 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.074 / Net I/σ(I): 16.3
Reflection shell	Resolution: 2.2→2.32 Å / R_merge(I) obs: 0.559 / Num. unique obs: 8720 / CC_1/2: 0.847

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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: 2.2→46 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.91 / SU B: 7.931 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.345 / ESU R Free: 0.239
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2582	3100	5.103 %
R_work	0.2083	57650	-
all	0.211	-	-
obs	-	60750	99.859 %

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: 47.019 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.004 Å²	-0 Å²	0.062 Å²
2-	-	0.075 Å²	0 Å²
3-	-	-	-0.084 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9335	0	176	375	9886

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	9751
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	9078
X-RAY DIFFRACTION	r_angle_refined_deg	1.476	1.646	13303
X-RAY DIFFRACTION	r_angle_other_deg	1.27	1.576	20931
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.91	5	1190
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.584	22.232	457
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.304	15	1565
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.163	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1331
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	10906
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2166
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	1956
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	8676
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	4786
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	4488
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.199	0.2	507
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.234	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.208	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.251	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.351	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	4.507	4.856	4790
X-RAY DIFFRACTION	r_mcbond_other	4.503	4.855	4789
X-RAY DIFFRACTION	r_mcangle_it	6.407	7.264	5970
X-RAY DIFFRACTION	r_mcangle_other	6.408	7.265	5971
X-RAY DIFFRACTION	r_scbond_it	4.41	5.122	4961
X-RAY DIFFRACTION	r_scbond_other	4.409	5.122	4962
X-RAY DIFFRACTION	r_scangle_it	6.484	7.532	7333
X-RAY DIFFRACTION	r_scangle_other	6.484	7.532	7334
X-RAY DIFFRACTION	r_lrange_it	9.254	55.903	11153
X-RAY DIFFRACTION	r_lrange_other	9.261	55.9	11081
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	9835
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.1	0.05	9813
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.102	0.05	9052
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.104	0.05	9837
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.098	0.05	9091
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.107	0.05	9015

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	0.09756	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09756	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10001	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.10001	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10196	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.10196	0.05008
4	7	B	X-RAY DIFFRACTION	Local ncs	0.1041	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.1041	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.09762	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.09762	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.10681	0.05008
6	12	D	X-RAY DIFFRACTION	Local ncs	0.10681	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 (%)
2.2-2.257	0.347	219	0.283	4191	X-RAY DIFFRACTION	98.3058
2.257-2.319	0.326	235	0.27	4073	X-RAY DIFFRACTION	100
2.319-2.386	0.295	236	0.246	4013	X-RAY DIFFRACTION	100
2.386-2.46	0.3	203	0.242	3923	X-RAY DIFFRACTION	100
2.46-2.54	0.313	186	0.242	3797	X-RAY DIFFRACTION	100
2.54-2.629	0.295	201	0.23	3658	X-RAY DIFFRACTION	100
2.629-2.729	0.275	199	0.23	3519	X-RAY DIFFRACTION	100
2.729-2.84	0.283	196	0.237	3385	X-RAY DIFFRACTION	100
2.84-2.966	0.291	196	0.227	3294	X-RAY DIFFRACTION	100
2.966-3.111	0.289	150	0.231	3131	X-RAY DIFFRACTION	100
3.111-3.279	0.278	159	0.216	2973	X-RAY DIFFRACTION	100
3.279-3.478	0.26	165	0.216	2829	X-RAY DIFFRACTION	100
3.478-3.718	0.232	143	0.199	2650	X-RAY DIFFRACTION	100
3.718-4.015	0.211	133	0.179	2467	X-RAY DIFFRACTION	100
4.015-4.398	0.205	108	0.173	2301	X-RAY DIFFRACTION	100
4.398-4.917	0.226	123	0.163	2079	X-RAY DIFFRACTION	100
4.917-5.676	0.241	80	0.181	1847	X-RAY DIFFRACTION	100
5.676-6.949	0.226	69	0.187	1576	X-RAY DIFFRACTION	100
6.949-9.815	0.197	63	0.165	1239	X-RAY DIFFRACTION	100
9.815-46	0.282	36	0.257	705	X-RAY DIFFRACTION	98.8

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