PDB-4h6k: W116I mutant of OYE1

ID or keywords:

Entry

Database: PDB / ID: 4h6k

Title

W116I mutant of OYE1

Components

NADPH dehydrogenase 1

Keywords

OXIDOREDUCTASE /

carvone /

enantioselectivity / flipped binding mode / enoate reductase /

biocatalysis / alkene reductase / semi rational design /

tim barrel / alpha/beta barrel

Function / homology

Function and homology information

NADPH dehydrogenase / pentaerythritol trinitrate reductase activity /

NADPH dehydrogenase activity / FMN binding
Similarity search - Function

Biological species

Saccharomyces pastorianus (lager yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Pompeu, Y.A. / Stewart, J.D.

Citation

Journal: ACS CATALYSIS / Year: 2013
Title: X‑ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in an Alkene Reductase
Authors: Pompeu, Y.A. / Sullivan, B. / Stewart, J.D.

History

Deposition	Sep 19, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Nov 29, 2023	Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4h6k.cif.gz	181.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4h6k.ent.gz	143.5 KB	Display	PDB format
PDBx/mmJSON format	4h6k.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h6/4h6k ftp://data.pdbj.org/pub/pdb/validation_reports/h6/4h6k	HTTPS FTP

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Related structure data

Related structure data	3txzC 4gbuC 4ge8C 4gweC 4gxmC 4k7vC 4k7yC 4k8eC 4k8hC 3rndS 3tx9 4h4i S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3tx9-1 3rnd-1 4k7y-1 5v4p-3 4ge8-1 4h4i-1 4k8h-1 4k8e-1 4k7v-1 1oyc-1 4gbu-1 Search similar-shape structures by Omokage search (details) 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: NADPH dehydrogenase 1

hetero molecules

45.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NADPH dehydrogenase 1

hetero molecules

A: NADPH dehydrogenase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	140.930, 140.930, 42.460
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

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Protein , 1 types, 1 molecules A

#1: Protein	NADPH dehydrogenase 1 / / Old yellow enzyme 1 Mass: 44867.395 Da / Num. of mol.: 1 / Mutation: W116I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces pastorianus (lager yeast) Gene: OYE1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q02899, NADPH dehydrogenase

#1: Protein

NADPH dehydrogenase 1 /

/ Old yellow enzyme 1

Mass: 44867.395 Da / Num. of mol.: 1 / Mutation: W116I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: Q02899,

NADPH dehydrogenase

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Non-polymers , 5 types, 318 molecules

#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.35 Å³/Da / Density % sol: 47.65 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.1M hepes, 0.2M MgCl2, peg400 35%, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 15, 2011
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.55→32.32 Å / Num. obs: 62580 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 9.1 % / B_iso Wilson estimate: 25 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shell	Resolution: 1.55→1.63 Å / Redundancy: 8.7 % / R_merge(I) obs: 0.916 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9018 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
CBASS		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3RND

3rnd

Resolution: 1.55→31.513 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 21.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2043	6248	10 %	random
R_work	0.1822	-	-	-
obs	0.1844	62493	99.9 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.55→31.513 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3172	0	56	313	3541

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3359
X-RAY DIFFRACTION	f_angle_d	1.047	4556
X-RAY DIFFRACTION	f_dihedral_angle_d	16.046	1244
X-RAY DIFFRACTION	f_chiral_restr	0.081	468
X-RAY DIFFRACTION	f_plane_restr	0.004	595

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 (%)
1.55-1.5676	0.3149	207	0.2872	1864	X-RAY DIFFRACTION	100
1.5676-1.5861	0.3159	201	0.2858	1805	X-RAY DIFFRACTION	99
1.5861-1.6054	0.2941	203	0.2622	1839	X-RAY DIFFRACTION	100
1.6054-1.6257	0.3196	206	0.2684	1856	X-RAY DIFFRACTION	100
1.6257-1.6471	0.3175	207	0.263	1853	X-RAY DIFFRACTION	100
1.6471-1.6697	0.3159	203	0.2509	1828	X-RAY DIFFRACTION	100
1.6697-1.6935	0.2508	209	0.2364	1882	X-RAY DIFFRACTION	100
1.6935-1.7188	0.2713	203	0.2162	1827	X-RAY DIFFRACTION	100
1.7188-1.7457	0.2443	206	0.2162	1852	X-RAY DIFFRACTION	100
1.7457-1.7743	0.2297	207	0.2162	1869	X-RAY DIFFRACTION	100
1.7743-1.8049	0.2545	204	0.2078	1837	X-RAY DIFFRACTION	100
1.8049-1.8377	0.231	207	0.2032	1860	X-RAY DIFFRACTION	100
1.8377-1.873	0.2287	205	0.2022	1847	X-RAY DIFFRACTION	100
1.873-1.9113	0.2301	209	0.1937	1872	X-RAY DIFFRACTION	100
1.9113-1.9528	0.242	205	0.1986	1848	X-RAY DIFFRACTION	100
1.9528-1.9982	0.216	208	0.1947	1870	X-RAY DIFFRACTION	100
1.9982-2.0482	0.2368	206	0.1877	1855	X-RAY DIFFRACTION	100
2.0482-2.1036	0.2182	208	0.1772	1877	X-RAY DIFFRACTION	100
2.1036-2.1655	0.2068	208	0.184	1876	X-RAY DIFFRACTION	100
2.1655-2.2353	0.1892	208	0.1691	1880	X-RAY DIFFRACTION	100
2.2353-2.3152	0.2033	207	0.1727	1854	X-RAY DIFFRACTION	100
2.3152-2.4079	0.2016	208	0.1749	1871	X-RAY DIFFRACTION	100
2.4079-2.5174	0.2045	209	0.1721	1896	X-RAY DIFFRACTION	100
2.5174-2.6501	0.2138	210	0.1692	1886	X-RAY DIFFRACTION	100
2.6501-2.816	0.2215	210	0.1666	1884	X-RAY DIFFRACTION	100
2.816-3.0333	0.186	213	0.1658	1909	X-RAY DIFFRACTION	100
3.0333-3.3382	0.1613	210	0.1765	1896	X-RAY DIFFRACTION	100
3.3382-3.8206	0.1821	215	0.158	1931	X-RAY DIFFRACTION	100
3.8206-4.8108	0.1573	217	0.1511	1956	X-RAY DIFFRACTION	100
4.8108-31.5194	0.1979	229	0.1985	2065	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	0.2726	0.1983	0.1336	0.2985	0.1828	0.0742	0.1272	-0.0968	0.106	0.1571	-0.1991	0.1136	-0.1091	-0.0095	-0.0024	0.2087	-0.0424	0.0203	0.3051	-0.0251	0.1408	-18.0232	44.6275	-0.9644
2	0.2237	0.1706	0.3038	0.1744	0.2374	0.3182	0.1967	-0.0419	-0.05	0.1141	-0.1265	-0.2343	-0.0531	0.0043	0.0131	0.1596	-0.0266	-0.0129	0.2081	0.0044	0.2225	4.8098	42.2727	-3.8539
3	0.3627	0.1354	0.3169	0.5236	0.1178	0.1581	0.1985	-0.0846	-0.3381	0.2848	-0.1288	-0.5064	0.1042	-0.0394	0.0168	0.1678	-0.052	-0.0263	0.2707	-0.0233	0.2644	6.2769	38.1888	-1.411
4	0.2147	0.0734	0.1463	0.438	0.041	0.1411	-0.1275	0.5332	-0.4502	-0.3068	0.1151	-0.6318	0.0987	0.3495	-0.0091	0.1974	0.0382	0.0251	0.3778	-0.2136	0.6913	11.774	24.5137	-21.1157
5	0.2806	0.1813	-0.1036	0.1389	-0.1116	0.233	0.2634	-0.2495	-0.722	0.2855	-0.0107	-0.356	0.0096	0.1613	0.2388	0.1939	-0.0413	-0.3737	0.2624	0.099	0.5931	9.3408	23.4675	0.5643
6	1.023	0.8434	-0.0558	0.4448	0.1082	0.3196	0.1657	0.0067	-0.5944	0.1491	-0.0631	-0.4642	0.1374	-0.0319	0.1189	0.2143	-0.0339	-0.0887	0.2002	-0.0052	0.3918	-3.7485	21.0228	-7.3078
7	0.8823	-0.297	0.0364	0.701	0.5085	0.5736	0.3906	0.3905	-0.0381	-0.1135	-0.4082	-0.2585	-0.3493	0.0293	-0.0007	0.2066	-0.1139	-0.0094	0.2894	0.0131	0.1753	-10.1773	32.7392	-10.3304
8	0.4824	0.2063	0.1944	0.2677	0.1154	0.1971	0.0837	0.0167	0.0319	-0.0725	-0.0486	0.0578	0.0048	-0.1513	0.0161	0.1715	-0.0344	-0.0053	0.2353	-0.0189	0.1135	-17.3521	37.5888	-6.5214
9	0.1175	0.1267	0.0939	0.1188	0.0835	0.0513	0.081	0.1583	0.2569	-0.0771	-0.101	-0.1221	-0.0839	-0.0425	-0	0.1988	0.0089	0.0333	0.2434	-0.0036	0.2103	-5.4216	55.1362	-11.1522

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 90 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 91 through 130 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 162 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 163 through 183 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 184 through 277 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 278 through 303 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 304 through 362 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 363 through 399 )

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