PDB-6p2i: Acyclic imino acid reductase (Bsp5) in complex with NADPH and D-Arg

ID or keywords:

Entry

Database: PDB / ID: 6p2i

Title

Acyclic imino acid reductase (Bsp5) in complex with NADPH and D-Arg

Components

Glycerate dehydrogenase

Keywords

oxidoreductase /

biosynthetic protein /

Enzyme /

Complex / Imine reductase / Acyclic imine

Function / homology

Function and homology information

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function

Biological species

Bacillus sp. 5mfcol3.1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.63 Å

Authors

Guo, J. / Higgins, M.A. / Daniel-Ivad, P. / Ryan, K.S.

Funding support

Canada, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2019
Title: An Asymmetric Reductase That Intercepts Acyclic Imino Acids Producedin Situby a Partner Oxidase.
Authors: Guo, J. / Higgins, M.A. / Daniel-Ivad, P. / Ryan, K.S.

History

Deposition	May 21, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6p2i.cif.gz	277.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6p2i.ent.gz	225.1 KB	Display	PDB format
PDBx/mmJSON format	6p2i.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/p2/6p2i ftp://data.pdbj.org/pub/pdb/validation_reports/p2/6p2i	HTTPS FTP

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Related structure data

Related structure data	5tx7S S: Starting model for refinement
Similar structure data	4lcj-1 6v8a-1 4e5k-2 3baz-1 2h1s-2 4lcj-3 5v6q-1 5v7g-1 1qp8-d 2ome-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycerate dehydrogenase

B: Glycerate dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	71.303, 96.760, 102.860
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glycerate dehydrogenase / / Bsp5 Mass: 35981.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. 5mfcol3.1 (bacteria) / Gene: SAMN04488573_102884 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1I4FUG4
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-DAR / D-ARGININE / Arginine Type: D-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350, 0.2 M sodium tartrate dibasic

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.63→70.48 Å / Num. obs: 89107 / % possible obs: 99.8 % / Redundancy: 12 % / CC_1/2: 0.999 / R_pim(I) all: 0.027 / Net I/σ(I): 14.4
Reflection shell	Resolution: 1.63→1.66 Å / Num. unique obs: 4522 / CC_1/2: 0.828 / R_pim(I) all: 0.406

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Processing

Software

Name	Classification
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5TX7

5tx7

Resolution: 1.63→24.19 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.24

	R_factor	Num. reflection	% reflection
R_free	0.1938	4372	4.92 %
R_work	0.1565	-	-
obs	0.1583	88918	99.58 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.63→24.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4877	0	136	633	5646

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5212
X-RAY DIFFRACTION	f_angle_d	0.938	7101
X-RAY DIFFRACTION	f_dihedral_angle_d	8.08	4942
X-RAY DIFFRACTION	f_chiral_restr	0.058	827
X-RAY DIFFRACTION	f_plane_restr	0.005	890

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 (%)
1.63-1.6485	0.3049	128	0.2721	2797	X-RAY DIFFRACTION	100
1.6485-1.6679	0.287	167	0.2741	2775	X-RAY DIFFRACTION	100
1.6679-1.6883	0.3179	121	0.2501	2814	X-RAY DIFFRACTION	100
1.6883-1.7096	0.2575	143	0.2481	2766	X-RAY DIFFRACTION	100
1.7096-1.7321	0.2625	144	0.2431	2797	X-RAY DIFFRACTION	100
1.7321-1.7558	0.2235	150	0.2293	2783	X-RAY DIFFRACTION	100
1.7558-1.7809	0.2485	146	0.2114	2797	X-RAY DIFFRACTION	100
1.7809-1.8075	0.2399	143	0.2185	2778	X-RAY DIFFRACTION	99
1.8075-1.8357	0.2722	163	0.2132	2781	X-RAY DIFFRACTION	100
1.8357-1.8658	0.2452	152	0.2072	2773	X-RAY DIFFRACTION	100
1.8658-1.898	0.1856	146	0.1946	2778	X-RAY DIFFRACTION	99
1.898-1.9325	0.2291	166	0.1742	2797	X-RAY DIFFRACTION	100
1.9325-1.9696	0.222	135	0.1658	2790	X-RAY DIFFRACTION	100
1.9696-2.0098	0.2104	146	0.1635	2813	X-RAY DIFFRACTION	100
2.0098-2.0535	0.201	161	0.1665	2801	X-RAY DIFFRACTION	100
2.0535-2.1012	0.2024	125	0.169	2817	X-RAY DIFFRACTION	100
2.1012-2.1538	0.2318	168	0.1646	2802	X-RAY DIFFRACTION	100
2.1538-2.2119	0.2016	151	0.1574	2786	X-RAY DIFFRACTION	100
2.2119-2.277	0.1939	133	0.159	2834	X-RAY DIFFRACTION	100
2.277-2.3504	0.1822	123	0.1595	2803	X-RAY DIFFRACTION	99
2.3504-2.4344	0.2078	143	0.1563	2811	X-RAY DIFFRACTION	99
2.4344-2.5317	0.2001	142	0.1534	2840	X-RAY DIFFRACTION	100
2.5317-2.6468	0.1837	147	0.1531	2842	X-RAY DIFFRACTION	100
2.6468-2.7862	0.1991	141	0.1612	2850	X-RAY DIFFRACTION	100
2.7862-2.9604	0.1944	128	0.1528	2856	X-RAY DIFFRACTION	100
2.9604-3.1886	0.2103	160	0.1618	2820	X-RAY DIFFRACTION	99
3.1886-3.5086	0.1975	160	0.1477	2814	X-RAY DIFFRACTION	98
3.5086-4.0143	0.1641	125	0.1285	2910	X-RAY DIFFRACTION	100
4.0143-5.05	0.141	182	0.1133	2901	X-RAY DIFFRACTION	100
5.05-24.1926	0.1638	133	0.143	3020	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.9511	0.9154	-0.2119	1.2675	-0.4141	0.5332	0.0212	-0.1363	0.0639	0.1282	0.0426	0.3031	-0.0019	-0.1078	-0.0609	0.1973	0.0032	0.0393	0.1741	0.0076	0.2127	14.229	44.2547	31.3294
2	2.8513	0.6878	-1.708	1.1493	-1.4749	5.183	0.0696	-0.0871	0.1132	0.0029	-0.0702	-0.0163	-0.0195	0.0984	0.0142	0.1567	0.0096	-0.0098	0.0695	-0.0244	0.1737	43.9234	56.2159	29.6782
3	2.2948	0.4527	-0.0856	2.0317	0.4862	1.9298	0.075	-0.0444	0.545	0.0853	-0.0637	0.2146	-0.3628	-0.1241	0.0062	0.2133	0.0188	0.0319	0.1441	0.0026	0.2586	31.9828	64.0962	30.914
4	5.3905	2.2057	-3.0507	3.3417	-2.1726	5.8846	-0.0048	-0.1676	-0.2485	0.1658	-0.0317	-0.1039	0.2349	0.0138	0.0705	0.1999	-0.0066	-0.0104	0.1385	-0.0089	0.2248	20.9591	35.6787	34.2594
5	2.5288	0.0056	-0.2601	1.7058	0.27	2.2495	0.0767	0.3926	0.5384	-0.4903	0.17	-0.4593	-0.3985	0.3087	-0.1569	0.3187	-0.0548	0.1146	0.2424	0.0397	0.3627	72.6404	64.7493	9.8006
6	5.1764	-0.2091	-0.1622	0.9547	0.0348	0.8214	-0.0955	0.375	-0.0581	-0.0744	0.0299	0.1271	-0.0383	-0.1459	0.0694	0.1747	-0.0134	0.008	0.1777	0.0056	0.1301	38.4144	49.6496	18.3331
7	4.826	-0.1843	0.5572	5.6764	0.9357	4.3428	-0.0466	-0.1804	-0.7182	0.2586	-0.1502	-0.258	0.529	0.1891	0.2182	0.2134	0.0349	0.0088	0.1669	-0.0021	0.2788	56.1068	38.6046	20.7574
8	4.9853	0.2625	-0.6247	1.9964	1.7646	3.5044	-0.2351	0.5969	-0.5834	-0.2201	-0.0053	0.0849	0.2742	-0.0356	0.2132	0.2153	0.0013	0.0032	0.2683	-0.0809	0.2178	54.4079	40.1703	7.9726
9	1.8708	-0.0959	-0.017	2.2749	0.9188	2.377	0.0008	0.7887	-0.1709	-0.3324	-0.0176	0.2148	0.0235	-0.2524	0.0275	0.2124	-0.0143	-0.0249	0.4246	-0.045	0.1909	45.9926	49.0767	4.8381
10	2.4517	-1.8594	-1.3605	2.3934	-0.036	2.3928	0.0493	-0.0288	0.236	0.0487	-0.0219	-0.2932	-0.0948	0.2323	-0.0632	0.2155	-0.0281	-0.0122	0.1785	-0.0321	0.2794	71.5724	60.1535	21.5622

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 114 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 115 through 185 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 186 through 279 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 280 through 307 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 98 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 99 through 151 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 152 through 185 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 186 through 211 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 212 through 279 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 280 through 307 )

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