PDB-7mgn: Crystal structure of F501H/H506E variant of 2-ketopropyl coenzyme...

ID or keywords:

Entry

Database: PDB / ID: 7mgn

Title

Crystal structure of F501H/H506E variant of 2-ketopropyl coenzyme M oxidoreductase/carboxylase (2-KPCC) from Xanthobacter autotrophicus

Components

2-oxopropyl-CoM reductase, carboxylating

Keywords

OXIDOREDUCTASE / carboxylation / oxidation-reduction / carbon dioxide fixation / carbon-carbon bond / anion-binding / kinetics

Function / homology

Function and homology information

2-oxopropyl-CoM reductase (carboxylating) / 2-oxopropyl-CoM reductase (carboxylating) activity / propylene catabolic process
Similarity search - Function

Biological species

Xanthobacter autotrophicus PY2 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Zadvornyy, O.A. / Prussia, G. / Peters, J.W.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2021
Title: The unique Phe-His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S-C bond cleavage.
Authors: Prussia, G.A. / Shisler, K.A. / Zadvornyy, O.A. / Streit, B.R. / DuBois, J.L. / Peters, J.W.

History

Deposition	Apr 12, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jul 28, 2021	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Aug 18, 2021	Group: Advisory / Database references Category: citation / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7mgn.cif.gz	460.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7mgn.ent.gz	375 KB	Display	PDB format
PDBx/mmJSON format	7mgn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7mgn_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7mgn_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7mgn_validation.xml.gz	49.2 KB	Display
Data in CIF	7mgn_validation.cif.gz	70.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/7mgn ftp://data.pdbj.org/pub/pdb/validation_reports/mg/7mgn	HTTPS FTP

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Related structure data

Related structure data	7mgoC 2c3cS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1mok-1 1mok-2 2c3d-d 3q6j-d 5axb-d 5u8w-1 5nhg-1 4m52-1 5mux-3 1zmc-4 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
Related items in Molecule of the Month	#179 - Nov 2014 Methyl-coenzyme M Reductase similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (5) #154 - Oct 2012 Citric Acid Cycle similarity (5) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: 2-oxopropyl-CoM reductase, carboxylating

B: 2-oxopropyl-CoM reductase, carboxylating

hetero molecules

117 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)	87.006, 60.111, 105.140
Angle α, β, γ (deg.)	90.00, 100.52, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	2-oxopropyl-CoM reductase, carboxylating / Aliphatic epoxide carboxylation component II / NADPH:2-ketopropyl-CoM carboxylase/oxidoreductase / 2-KPCC Mass: 57396.285 Da / Num. of mol.: 2 / Mutation: F501H, H506E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus PY2 (bacteria) Strain: ATCC BAA-1158 / Py2 / Gene: xecC, Xaut_4867 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q56839, 2-oxopropyl-CoM reductase (carboxylating)
#2: Chemical	ChemComp-COM / 1-THIOETHANESULFONIC ACID Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₃S₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.36 Å³/Da / Density % sol: 47.89 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: containing 0.17 M ammonium acetate, 0.085 M trisodium citrate pH 5.6, 27% PEG 4,000, and 15% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.8→39.19 Å / Num. obs: 97751 / % possible obs: 98.4 % / Redundancy: 5.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.082 / R_pim(I) all: 0.037 / Χ²: 0.99 / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.84 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4647 / CC_1/2: 0.697 / R_pim(I) all: 0.422 / % possible all: 94.5

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4085	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2c3c

2c3c

Resolution: 1.8→37.66 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1888	4981	5.1 %
R_work	0.1406	-	-
obs	0.1431	97713	98.2 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→37.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8040	0	122	737	8899

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8393
X-RAY DIFFRACTION	f_angle_d	0.972	11389
X-RAY DIFFRACTION	f_dihedral_angle_d	14.811	3091
X-RAY DIFFRACTION	f_chiral_restr	0.059	1245
X-RAY DIFFRACTION	f_plane_restr	0.008	1485

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 (%)
1.8-1.82	0.3055	160	0.2716	2947	X-RAY DIFFRACTION	93
1.82-1.84	0.2925	162	0.2316	3041	X-RAY DIFFRACTION	99
1.84-1.86	0.2755	171	0.2224	3083	X-RAY DIFFRACTION	99
1.86-1.89	0.2536	178	0.2012	3096	X-RAY DIFFRACTION	99
1.89-1.91	0.2298	166	0.1864	3060	X-RAY DIFFRACTION	99
1.91-1.94	0.2333	164	0.1797	3136	X-RAY DIFFRACTION	98
1.94-1.97	0.2157	150	0.1692	3032	X-RAY DIFFRACTION	98
1.97-1.99	0.2253	157	0.1634	3144	X-RAY DIFFRACTION	99
1.99-2.03	0.2022	164	0.1577	3088	X-RAY DIFFRACTION	99
2.03-2.06	0.2124	163	0.1577	3065	X-RAY DIFFRACTION	98
2.06-2.09	0.2048	150	0.1554	3058	X-RAY DIFFRACTION	98
2.09-2.13	0.2178	151	0.1559	3004	X-RAY DIFFRACTION	95
2.13-2.17	0.2045	172	0.1479	3074	X-RAY DIFFRACTION	99
2.17-2.22	0.2106	167	0.1518	3141	X-RAY DIFFRACTION	99
2.22-2.27	0.2002	181	0.145	3044	X-RAY DIFFRACTION	99
2.27-2.32	0.2068	157	0.142	3134	X-RAY DIFFRACTION	99
2.32-2.38	0.2088	165	0.1466	3108	X-RAY DIFFRACTION	99
2.38-2.44	0.1903	148	0.1444	3122	X-RAY DIFFRACTION	99
2.44-2.51	0.2081	167	0.1441	3139	X-RAY DIFFRACTION	99
2.51-2.59	0.2108	173	0.1428	3065	X-RAY DIFFRACTION	98
2.59-2.69	0.2259	156	0.1443	3072	X-RAY DIFFRACTION	98
2.69-2.79	0.1819	168	0.1449	3047	X-RAY DIFFRACTION	97
2.79-2.92	0.204	193	0.1425	3099	X-RAY DIFFRACTION	99
2.92-3.08	0.1883	165	0.1377	3116	X-RAY DIFFRACTION	99
3.08-3.27	0.1758	183	0.1313	3117	X-RAY DIFFRACTION	99
3.27-3.52	0.1643	171	0.1281	3142	X-RAY DIFFRACTION	99
3.52-3.87	0.1358	162	0.1164	3081	X-RAY DIFFRACTION	98
3.87-4.43	0.1483	161	0.105	3132	X-RAY DIFFRACTION	98
4.43-5.58	0.1441	179	0.1155	3154	X-RAY DIFFRACTION	99
5.58-37.66	0.2081	177	0.1442	3191	X-RAY DIFFRACTION	97

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	0.8302	-0.0114	-0.0378	0.991	0.3691	0.4978	0.0041	0.2769	-0.0258	-0.2915	-0.0749	0.2871	-0.0178	-0.1986	0.0706	0.2938	-0.0155	-0.0701	0.3457	-0.007	0.2656	-5.951	2.724	119.201
2	0.8181	-0.0919	-0.1187	0.4678	0.0492	0.3379	-0.033	0.0036	-0.081	-0.0434	0.0111	0.0971	0.0478	-0.0622	0.0291	0.1663	-0.0268	0.0097	0.1895	-0.0002	0.19	5.048	-0.753	141.041
3	2.8207	-0.9098	-0.1695	0.8341	-0.1952	1.6277	0.0875	-0.4001	0.3792	0.0323	0.0397	-0.2861	-0.3085	0.0688	-0.1071	0.2161	-0.0493	0.0031	0.2509	-0.1032	0.3021	43.387	13.268	155.334
4	0.3832	0.0784	0.1004	1.4568	-0.7962	1.689	-0.0133	-0.1072	-0.0304	0.0911	0.0177	-0.1462	-0.0549	0.0291	0.0325	0.1221	-0.0179	0.0189	0.1923	-0.0281	0.2644	47.62	-3.141	147.087
5	1.0429	0.1696	0.2902	0.8499	-0.4871	0.7421	-0.0204	0.0482	0.1881	-0.0521	0.0355	-0.035	-0.114	0.0633	0.0046	0.2195	-0.0169	0.0527	0.1728	-0.0364	0.2226	27.063	18.839	137.207
6	2.4271	-0.342	-0.3215	0.8076	0.5172	1.0858	0.0409	-0.1739	0.0867	-0.0361	0.1068	-0.2102	-0.0325	0.1084	-0.1088	0.1438	-0.0281	0.0212	0.2247	-0.0426	0.2863	53.956	2.136	145.978
7	0.0555	0.2369	-0.3188	1.0569	-1.5697	2.351	0.024	-0.0268	0.0519	-0.2531	-0.0175	-0.1311	-0.1582	0.0566	-0.0016	0.2842	-0.0828	0.0731	0.2013	-0.0168	0.2788	44.005	23.117	128.605
8	0.9239	0.4625	0.24	0.7027	0.2882	0.7981	-0.0288	0.1334	0.0823	-0.2226	0.1181	-0.1032	-0.1579	0.0692	-0.0618	0.3507	-0.0636	0.0731	0.2014	0.0001	0.2201	32.285	23.795	117.932
9	1.1701	-1.4933	0.6	1.8927	-0.7321	0.3091	0.0893	0.0779	0.1884	-0.2338	-0.073	-0.287	-0.1042	0.1952	-0.0284	0.2934	-0.0694	0.1107	0.2582	-0.028	0.3054	49.902	12.321	126.773
10	1.6854	-0.5167	0.8384	0.456	-0.1353	0.5176	0.0537	0.1679	-0.0639	-0.1614	0.0363	-0.1481	0.019	0.0774	-0.101	0.2249	-0.0273	0.0729	0.2003	-0.0383	0.2374	40.603	-2.165	128.981
11	1.8132	-1.0028	-0.7627	2.044	0.5631	0.6054	0.0486	0.2208	-0.0111	-0.3633	0.0263	0.0488	-0.0435	-0.0691	-0.0399	0.2925	-0.033	-0.008	0.246	-0.0132	0.1496	13.645	4.57	114.846
12	0.6459	0.2615	-0.1469	1.4621	0.1966	0.866	-0.0296	0.1459	-0.1133	-0.2557	0.036	0.0869	0.0298	-0.0562	-0.0199	0.2502	-0.0233	0.0023	0.206	-0.0255	0.1623	14.965	-3.742	119.684

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:180 )	A	2 - 180
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 181:523 )	A	181 - 523
3	X-RAY DIFFRACTION	3	( CHAIN B AND RESID 2:35 )	B	2 - 35
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 36:73 )	B	36 - 73
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 74:146 )	B	74 - 146
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 147:180 )	B	147 - 180
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 181:208 )	B	181 - 208
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 209:304 )	B	209 - 304
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 305:335 )	B	305 - 335
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 336:401 )	B	336 - 401
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 402:442 )	B	402 - 442
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 443:523 )	B	443 - 523

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