PDB-5gwe: cytochrome P450 CREJ

ID or keywords:

Entry

Database: PDB / ID: 5gwe

Title

cytochrome P450 CREJ

Components

Cytochrome P450

Keywords

ELECTRON TRANSPORT / cytochrome P450 / Complex

Function / homology

Function and homology information

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function

Biological species

Corynebacterium glutamicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Dong, S. / liu, X. / Wang, X. / Feng, Y.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Selective oxidation of aliphatic C-H bonds in alkylphenols by a chemomimetic biocatalytic system
Authors: Du, L. / Dong, S. / Zhang, X. / Jiang, C. / Chen, J. / Yao, L. / Wang, X. / Wan, X. / Liu, X. / Wang, X. / Huang, S. / Cui, Q. / Feng, Y. / Liu, S.J. / Li, S.

History

Deposition	Sep 11, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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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Download

PDBx/mmCIF format	5gwe.cif.gz	691.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5gwe.ent.gz	571 KB	Display	PDB format
PDBx/mmJSON format	5gwe.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/gw/5gwe ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gwe	HTTPS FTP

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Related structure data

Related structure data	5xjnC 4rm4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6w0s-1 2yca-d 5xjn-d 3zsn-3 2ygx-1 4fb2-2 1y7p-1 2y5z-3 7ccf-d 3zsn-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) 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

Related structure data

5xjnC

4rm4S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Cytochrome P450

B: Cytochrome P450

C: Cytochrome P450

D: Cytochrome P450

hetero molecules

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

1

A: Cytochrome P450

hetero molecules

defined by author&software
46.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cytochrome P450

hetero molecules

defined by author&software
46.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Cytochrome P450

hetero molecules

defined by author&software
46.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Cytochrome P450

hetero molecules

defined by author&software
46.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.540, 121.140, 125.610
Angle α, β, γ (deg.)	90.000, 90.960, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1124- HOH
2	1	B-891- HOH

#1: Protein	Cytochrome P450 Mass: 45770.531 Da / Num. of mol.: 4 / Mutation: A96T, D382E, K422R, E433K, A452T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria) Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: Cgl0553 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NSW2
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Chemical	ChemComp-GWM / (4-methylphenyl) dihydrogen phosphate / phosphoric acid mono-p-tolyl ester Mass: 188.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₇H₉O₄P
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1825 / 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: 2.61 Å³/Da / Density % sol: 52.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: ammonium sulfate, sodium cacodylate trihydrate, PEG8000

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Data collection

Diffraction	Mean temperature: 173 K
Diffraction source	Source: SYNCHROTRON / Site: NFPSS / Beamline: BL17B / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2→34.561 Å / Num. obs: 125652 / % possible obs: 99.29 % / Redundancy: 2 % / CC_1/2: 0.992 / R_merge(I) obs: 0.06 / Net I/σ(I): 8.53
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 2 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 2.4 / % possible all: 96.48

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Processing

Software

Name	Version	Classification
MOSFLM		data collection
Aimless		data scaling
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.2	data extraction
ARP		model building
PHASER		phasing
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RM4

4rm4

Resolution: 2→34.561 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.32

	R_factor	Num. reflection	% reflection
R_free	0.1979	1998	1.59 %
R_work	0.1608	-	-
obs	0.1614	125652	99.27 %

Solvent computation

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

Displacement parameters

B_iso max: 119.92 Å² / B_iso mean: 34.05 Å² / B_iso min: 10.38 Å²

Refinement step

Cycle: final / Resolution: 2→34.561 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12754	0	255	1825	14834
B_iso mean	-	-	23.79	38.08	-
Num. residues	-	-	-	-	1609

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	13343
X-RAY DIFFRACTION	f_angle_d	1.223	18186
X-RAY DIFFRACTION	f_chiral_restr	0.056	1945
X-RAY DIFFRACTION	f_plane_restr	0.006	2355
X-RAY DIFFRACTION	f_dihedral_angle_d	13.548	4832

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.05	0.2915	138	0.2477	8474	8612	95
2.05-2.1054	0.2296	134	0.2156	8784	8918	100
2.1054-2.1674	0.2218	145	0.1928	8887	9032	100
2.1674-2.2373	0.2314	145	0.1827	8902	9047	100
2.2373-2.3173	0.253	138	0.1728	8818	8956	100
2.3173-2.41	0.2281	143	0.1689	8875	9018	100
2.41-2.5197	0.2209	145	0.1689	8867	9012	100
2.5197-2.6525	0.2392	142	0.1654	8847	8989	100
2.6525-2.8186	0.196	144	0.1669	8881	9025	100
2.8186-3.0361	0.2137	142	0.1689	8858	9000	100
3.0361-3.3414	0.2133	143	0.1622	8846	8989	100
3.3414-3.8244	0.1958	142	0.1432	8882	9024	99
3.8244-4.8163	0.1354	145	0.129	8828	8973	99
4.8163-34.5659	0.1582	152	0.1452	8890	9042	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	2.4306	-0.4189	-0.1342	3.28	-0.1463	2.3083	0.0334	-0.0724	0.1865	-0.1347	-0.05	-0.321	-0.1856	0.1896	-0.0007	0.1031	-0.0204	0.0161	0.1426	0.0021	0.1479	85.409	92.6632	44.1636
2	2.242	-0.4636	-1.9183	2.1011	0.6074	2.6581	-0.0426	-0.0261	-0.1332	-0.211	-0.135	-0.1129	0.0982	0.0422	0.1457	0.1209	0.0494	0.0137	0.1288	0.0113	0.1487	78.2944	71.6237	50.7881
3	7.1739	-4.0117	-2.1171	7.5807	2.7547	7.8622	-0.1862	0.0704	-0.859	-0.1639	0.0035	0.6591	1.0594	-0.1412	0.0902	0.4456	-0.1126	-0.0776	0.3197	-0.0548	0.3123	57.6581	74.388	28.6578
4	1.1503	-0.0065	0.0548	0.8709	-0.4719	1.6351	0.0124	0.1291	-0.1962	-0.1469	-0.0704	0.1521	0.1332	-0.1551	0.0448	0.1436	0.0007	0.0266	0.1743	-0.058	0.1822	65.5899	73.4061	44.88
5	2.7254	-0.215	1.8476	1.4053	-0.1252	3.667	0.0134	0.2177	0.1929	-0.2858	-0.132	-0.0444	-0.19	0.0457	0.1355	0.1959	0.0628	0.0534	0.1432	0.0187	0.1638	79.2762	90.1541	32.4532
6	2.5151	-0.3087	0.7099	1.2249	0.4072	2.1547	0.0144	0.207	0.1502	-0.2666	-0.1407	0.1546	-0.0764	-0.2301	0.1127	0.2188	0.0309	0.02	0.1729	0.0012	0.1539	65.3464	86.6628	33.3677
7	1.3851	0.1839	0.643	1.8575	-0.4304	3.3769	-0.5352	0.4682	0.1617	-0.3099	-0.1208	0.0321	-0.0065	0.6336	0.1509	0.4185	-0.2135	-0.1057	0.3799	0.032	0.2469	84.5438	27.0697	16.2289
8	1.2648	0.978	-0.2177	1.7806	-0.6004	2.6447	-0.305	0.2087	0.3405	-0.1794	-0.1644	0.6553	-0.6326	-0.6342	0.2035	0.4592	0.0678	-0.2663	0.4036	-0.1273	0.6521	65.5315	35.1727	19.9357
9	2.3614	0.283	1.0188	2.0743	0.1159	4.0804	-0.1701	0.0551	0.0841	0.0337	-0.1799	0.1283	0.1839	0.2473	0.2133	0.2064	-0.0627	0.0037	0.1592	-0.0154	0.1995	82.5214	21.9661	30.0808
10	5.7052	1.4742	-0.4293	2.0824	-0.0944	2.5925	-0.267	-0.2335	0.1819	-0.0142	-0.0823	0.5441	0.1889	-0.6343	0.2985	0.2582	-0.0835	0.0019	0.3704	-0.1038	0.4229	64.3073	20.5804	30.1666
11	3.305	-0.4735	-0.1015	2.4452	-0.0384	2.3419	-0.0764	-0.1421	-0.2065	-0.0443	0.0075	0.2085	0.2073	-0.1757	0.0527	0.1283	-0.0177	0.0079	0.106	-0.0083	0.1339	87.5339	31.7215	50.1339
12	2.7046	-0.6833	0.4265	2.7974	-2.2428	2.8638	-0.1196	-0.211	0.023	-0.1457	-0.1472	-0.244	0.2002	0.1837	0.2167	0.118	0.0457	0.0242	0.1329	-0.0048	0.1671	108.2468	39.8054	43.4285
13	5.1311	-1.6777	2.1831	8.0339	-1.1384	7.2931	0.0389	-0.064	0.45	0.0511	0.0896	-1.061	-0.2758	1.1003	-0.1148	0.3318	-0.0788	-0.0585	0.4897	-0.1755	0.4319	104.5431	60.4189	65.4926
14	2.8707	-0.6225	-0.8141	2.3236	0.2179	3.4394	0.0908	0.0978	0.9142	-0.0615	-0.0196	-0.3028	-0.5281	-0.0263	-0.0544	0.2965	-0.0122	-0.0891	0.1861	-0.0125	0.3656	99.3762	61.9493	56.8485
15	2.4097	-0.8129	-0.1736	1.5427	-0.2446	1.6137	-0.077	-0.2379	0.2373	0.0657	-0.0339	-0.4471	-0.1183	0.1955	0.1006	0.1496	-0.0074	-0.0204	0.1654	0.0448	0.2727	110.5305	50.3233	44.3943
16	1.622	-1.106	-1.9997	1.4901	0.6292	3.2882	0.0048	0.0348	0.1317	0.0237	-0.0232	-0.0727	-0.1623	-0.0186	0.0258	0.1396	0.0126	-0.0788	0.1667	-0.0142	0.2133	101.0322	49.1744	54.3448
17	1.1086	0.2551	0.2864	1.8268	0.5572	1.9767	-0.1123	-0.2676	0.0646	0.1135	-0.014	0.0577	-0.0752	-0.1397	0.121	0.1066	0.0566	-0.0229	0.2104	0.0224	0.1416	92.6391	40.5656	62.5474
18	1.8587	-0.7023	-0.0377	3.0432	1.316	2.3676	-0.1639	-0.1779	0.2038	0.1356	0.0041	0.2546	-0.3598	-0.3763	0.1174	0.2045	0.1018	-0.0252	0.2385	-0.0169	0.2399	85.565	56.9989	57.0274
19	0.5027	-0.2354	-0.0673	1.7879	-0.1643	2.2769	0.2484	0.2682	0.2626	-0.3951	-0.1955	0.0139	-0.5121	-0.4584	-0.111	0.3814	0.1549	0.1056	0.3193	0.0823	0.2229	85.9359	79.2502	12.6043
20	2.9631	0.422	-0.3623	2.8536	-2.2748	4.1224	-0.0293	0.325	0.1925	-0.1471	0.0098	-0.2974	-0.2903	0.2257	-0.0327	0.2115	-0.0496	0.065	0.189	-0.0207	0.2745	106.9524	72.8748	19.4305
21	8.5387	1.7188	0.0363	5.1953	1.5981	5.8865	0.4143	0.5724	-0.005	-0.002	-0.0695	-0.5972	0.3392	0.9317	-0.3923	0.6728	0.2624	0.0907	0.5243	-0.0297	0.3639	105.079	52.3959	-2.7974
22	1.5334	-0.4251	0.4971	1.1696	0.1031	2.5896	0.1115	0.2117	-0.0092	-0.2566	0.0093	-0.2686	0.1427	0.2989	-0.0882	0.2533	0.0299	0.094	0.2006	0.023	0.2588	105.6769	60.2046	13.4938
23	1.3089	-0.3761	-0.6376	2.1114	1.0979	2.6774	0.2264	0.4002	0.0957	-0.5713	-0.1475	-0.0504	-0.3359	-0.4322	-0.0326	0.4347	0.1001	0.0677	0.3768	0.1002	0.2074	91.2151	70.7643	0.3924
24	3.7399	0.9511	0.8787	9.1902	5.933	3.942	-0.0335	0.352	-0.4542	-0.2741	-0.0161	0.569	0.3933	-0.4781	0.0956	0.4849	-0.0855	-0.0059	0.3797	0.063	0.2588	85.656	53.8717	5.8688

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 51 through 109 )	A	51 - 109
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 110 through 155 )	A	110 - 155
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 156 through 178 )	A	156 - 178
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 179 through 310 )	A	179 - 310
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 311 through 392 )	A	311 - 392
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 393 through 455 )	A	393 - 455
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 51 through 163 )	B	51 - 163
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 164 through 310 )	B	164 - 310
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 311 through 405 )	B	311 - 405
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 406 through 455 )	B	406 - 455
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 51 through 109 )	C	51 - 109
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 110 through 155 )	C	110 - 155
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 156 through 178 )	C	156 - 178
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 179 through 207 )	C	179 - 207
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 208 through 278 )	C	208 - 278
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 279 through 310 )	C	279 - 310
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 311 through 423 )	C	311 - 423
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 424 through 455 )	C	424 - 455
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 53 through 109 )	D	53 - 109
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 110 through 155 )	D	110 - 155
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 156 through 178 )	D	156 - 178
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 179 through 310 )	D	179 - 310
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 311 through 423 )	D	311 - 423
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 424 through 455 )	D	424 - 455

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Yorodumi