PDB-7pkx: Crystal structure of a DyP-type peroxidase from Bacillus subtilis...

ID or keywords:

Entry

Database: PDB / ID: 7pkx

Title

Crystal structure of a DyP-type peroxidase from Bacillus subtilis in P3121 space group

Components

Deferrochelatase/peroxidase

Keywords

OXIDOREDUCTASE / Dye-decolorizing Peroxidase / Bacillus subtilis / phenolic compounds / protein crystallography / heme proteins

Function / homology

Function and homology information

iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.491 Å

Authors

Borges, P.T. / Rodrigues, C. / Silva, D. / Taborda, A. / Brissos, V. / Frazao, C. / Martins, L.O.

Funding support

United Kingdom, 3items

Organization	Grant number	Country
H2020 Marie Curie Actions of the European Commission	B-LigZymes H2020-MSCA-RISE 2018	United Kingdom
Foundation for Science and Technology (FCT)	PTDC/BBBEBB/0122/2014	United Kingdom
Foundation for Science and Technology (FCT)	PTDC/BII-BBF/29564/2017	United Kingdom

Citation

Journal: Int J Mol Sci / Year: 2021
Title: Loops around the Heme Pocket Have a Critical Role in the Function and Stability of Bs DyP from Bacillus subtilis .
Authors: Rodrigues, C.F. / Borges, P.T. / Scocozza, M.F. / Silva, D. / Taborda, A. / Brissos, V. / Frazao, C. / Martins, L.O.

History

Deposition	Aug 27, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	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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Download

PDBx/mmCIF format	7pkx.cif.gz	291.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7pkx.ent.gz	237.9 KB	Display	PDB format
PDBx/mmJSON format	7pkx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7pkx_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7pkx_full_validation.pdf.gz	1.2 MB	Display
Data in XML	7pkx_validation.xml.gz	26.4 KB	Display
Data in CIF	7pkx_validation.cif.gz	35.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pk/7pkx ftp://data.pdbj.org/pub/pdb/validation_reports/pk/7pkx	HTTPS FTP

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Related structure data

Related structure data	7pl0C 4grcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6kmm-1 7pl0-2 6i8e-d 6i8i-d 6i91-d 6i8o-d 6i8p-d 6kmn-2 6i43-d 7pl0-1 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
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (3) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: Deferrochelatase/peroxidase

B: Deferrochelatase/peroxidase

hetero molecules

92.7 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)	95.271, 95.271, 181.244
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain C
2	1	chain D
1	2	(chain A and (resid 56 through 110 or resid 117 through 411 or resid 413 through 414))
2	2	(chain B and (resid 56 through 411 or resid 413 through 414))

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain C	C	501
2	1	1	chain D	D	501
1	1	2	(chain A and (resid 56 through 110 or resid 117 through 411 or resid 413 through 414))	A	56 - 110
1	2	2	(chain A and (resid 56 through 110 or resid 117 through 411 or resid 413 through 414))	A	117 - 411
1	3	2	(chain A and (resid 56 through 110 or resid 117 through 411 or resid 413 through 414))	A	413 - 414
2	1	2	(chain B and (resid 56 through 411 or resid 413 through 414))	B	56 - 411
2	2	2	(chain B and (resid 56 through 411 or resid 413 through 414))	B	413 - 414

NCS ensembles :

ID
1
2

#1: Protein	Deferrochelatase/peroxidase Mass: 45751.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2151, CFD21_01545 / Production host: Escherichia coli (E. coli) References: UniProt: A0A162R372, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.04 Å³/Da / Density % sol: 59.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.05 M potassium phosphate monobasic and 15% (w/v) PEG 8K

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 2.491→75.092 Å / Num. obs: 33961 / % possible obs: 99.7 % / Redundancy: 6.3 % / B_iso Wilson estimate: 61.42 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.056 / R_rim(I) all: 0.168 / R_sym value: 0.13 / Net I/σ(I): 10.37
Reflection shell	Resolution: 2.491→2.59 Å / Num. unique obs: 5374 / CC_1/2: 0.306

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data scaling
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4GRC

4grc

Resolution: 2.491→75.092 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.55 / Stereochemistry target values: LS_WUNIT_K1
Details: BsDyP refinement converged to Rwork and Rfree of 0.207 and 0.232, respectively using a Rfree test set size of 1.48 % (503 reflections). The final model was refined versus the full data, ...

	R_factor	Num. reflection	% reflection
R_free	0.1931	503	100 %
R_work	0.1931	33961	-
obs	0.1931	33961	99.7 %

Solvent computation

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

Displacement parameters

B_iso max: 152.72 Å² / B_iso mean: 67.9682 Å² / B_iso min: 20 Å²

Refinement step

Cycle: final / Resolution: 2.491→75.092 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5499	0	86	28	5613
B_iso mean	-	-	59.32	51.84	-
Num. residues	-	-	-	-	707

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms: 6.217 / Type: TORSIONAL

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Number
1	1	A	A	3372
1	2	B	B	3372
2	1	C	A	16
2	2	D	B	16

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.491-2.59	0.4197	1072	0.4197	1072	97
2.5191-2.5487	0.3876	1107	0.3876	1107	99
2.5487-2.5798	0.3767	1137	0.3767	1137	100
2.5798-2.6125	0.3774	1098	0.3774	1098	100
2.6125-2.6468	0.3689	1120	0.3689	1120	100
2.6468-2.6831	0.3415	1105	0.3415	1105	100
2.6831-2.7214	0.3378	1136	0.3378	1136	100
2.7214-2.7621	0.3393	1097	0.3393	1097	100
2.7621-2.8052	0.3277	1138	0.3277	1138	100
2.8052-2.8512	0.3079	1116	0.3079	1116	100
2.8512-2.9004	0.3078	1119	0.3078	1119	100
2.9004-2.9531	0.2925	1110	0.2925	1110	100
2.9531-3.0099	0.2761	1115	0.2761	1115	100
3.0099-3.0714	0.2778	1146	0.2778	1146	100
3.0714-3.1382	0.2528	1105	0.2528	1105	100
3.1382-3.2112	0.2412	1127	0.2412	1127	100
3.2112-3.2915	0.244	1135	0.244	1135	100
3.2915-3.3805	0.2296	1116	0.2296	1116	100
3.3805-3.4799	0.2091	1122	0.2091	1122	100
3.4799-3.5922	0.1875	1149	0.1875	1149	100
3.5922-3.7206	0.1761	1117	0.1761	1117	100
3.7206-3.8696	0.1676	1136	0.1676	1136	100
3.8696-4.0457	0.1561	1137	0.1561	1137	100
4.0457-4.259	0.1392	1135	0.1392	1135	100
4.259-4.5258	0.1351	1164	0.1351	1164	100
4.5258-4.8752	0.124	1143	0.124	1143	100
4.8752-5.3656	0.1364	1154	0.1364	1154	100
5.3656-6.1418	0.1508	1165	0.1508	1165	100
6.1418-7.7367	0.1465	1183	0.1465	1183	100
7.7367-75.09	0.1496	1257	0.1496	1257	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	0.016	0.0612	-0.1288	-0.0145	0.0204	0.2191	-0.2069	-0.0777	0.1167	0.2405	-0.041	-0.1365	-0.1757	-0.3715	0	0.5091	-0.0616	0.052	0.4352	-0.0578	0.5223	26.4344	-5.6135	-7.2643
2	0.6973	-0.0976	0.2831	-0.013	0.0516	0.2634	-0.3157	0.1926	-0.2666	0.0504	0.163	-0.1661	0.4373	-0.0266	0.0003	0.5427	-0.0724	0.0992	0.5015	-0.0307	0.5427	24.8216	-22.978	-4.0222
3	0.1896	0.2223	0.1305	-0.1258	-0.0478	-0.0105	-0.1266	-0.1033	0.2312	0.1395	0.0745	-0.0172	-0.2097	-0.2241	-0.0001	0.6203	0.0331	0.0343	0.6368	-0.0201	0.5071	25.3168	-14.3266	6.7721
4	0.3546	0.1763	0.5174	-0.0847	0.0822	0.3808	-0.1367	-0.3347	0.1376	0.0184	0.0231	-0.0112	0.1092	-0.0493	0	0.6426	-0.0858	0.0153	0.5957	-0.0035	0.514	33.6545	-16.8748	3.4964
5	0.1542	0.037	0.0962	0.0705	-0.0565	0.1152	0.1215	0.6927	0.1544	-0.0049	0.4775	-0.1609	1.1486	0.1242	-0.0029	0.827	-0.118	-0.0096	0.8058	0.0023	0.7839	8.7498	-27.6529	-3.0087
6	0.0423	0.0058	-0.029	0.0101	0.0124	-0.0021	-0.1756	0.5938	-0.3448	0.3153	0.2355	-0.0745	-0.6289	-0.9247	0.0011	0.9747	-0.2023	0.2063	0.8911	-0.0459	0.8384	5.7636	-26.3852	0.9369
7	0.6757	0.3493	0.3478	0.5694	-0.0132	0.9008	0.0632	-0.068	0.0939	0.1368	0.0342	0.0812	0.2144	-0.1806	-0.0001	0.5036	-0.056	0.0262	0.4464	0.0212	0.4858	23.6113	-23.9963	-7.6935
8	0.0852	0.3045	-0.2146	1.3858	-0.3025	1.2086	0.2269	0.0016	0.0478	-0.251	-0.0233	0.1338	-0.1665	-0.0516	-0.0001	0.5404	0.0508	0.0034	0.4252	-0.0014	0.5516	24.8184	-8.6067	-21.7074
9	0.0853	-0.0467	-0.0597	0.3798	-0.3656	0.3303	-0.2625	-0.3318	-0.0048	0.0209	0.3172	0.2389	0.3718	0.0869	0.0001	0.4855	0.0068	0.0427	0.458	0.0271	0.5787	20.3812	-20.8084	-16.4187
10	0.4889	-0.1034	-0.3593	0.0778	-0.0851	0.3595	0.1211	0.1624	-0.088	-0.2083	-0.2924	0.3696	0.3627	0.0237	-0.0002	0.6966	0.0402	-0.0301	0.4762	0.0131	0.5389	32.132	-22.1237	-37.9225
11	1.3735	-1.0333	-0.8324	0.867	0.9479	0.9205	0.1696	-0.0605	-0.024	-0.1924	-0.1238	0.1613	-0.2212	-0.1032	0	0.6099	-0.0742	-0.0436	0.4706	0.0243	0.512	24.9431	-14.5232	-32.1279
12	0.2526	-0.9473	0.4343	0.3297	-0.4761	0.1755	0.0134	0.2728	0.0082	0.5601	-0.2381	0.1895	0.3947	-0.206	0.0006	0.5639	-0.0409	-0.0069	0.4266	-0.0218	0.5935	27.2966	-26.3636	-20.2343
13	0.7402	0.6969	0.2945	1.009	-0.217	0.4208	-0.0259	0.0217	-0.0054	0.1427	-0.1038	0.2962	0.4026	-0.5124	-0	0.482	-0.0445	0.005	0.4307	-0.0025	0.5328	16.5016	-19.0426	-15.232
14	0.2809	-0.0017	-0.0312	0.0009	0.0124	0.2509	-0.2299	0.0437	0.2372	0.0263	-0.0268	-0.0414	-0.161	0.5044	0.0001	0.5953	-0.0324	0.0886	0.6484	0.0284	0.6208	60.2896	-18.7542	-18.8209
15	0.2913	0.0347	-0.3646	0.1515	-0.0751	0.3273	-0.3207	0.0773	-0.0044	0.5637	0.3768	0.1852	0.5477	0.3514	-0	0.5725	0.1099	0.0297	0.4107	-0.0395	0.4991	49.9477	-33.028	-21.0354
16	0.1426	-0.467	0.0026	0.5061	0.1255	-0.0911	-0.1126	0.1579	0.1937	-0.284	0.0157	-0.0645	0.1217	0.4569	-0.0004	0.4555	0.054	-0.0022	0.513	0.0763	0.3478	55.4995	-27.2696	-32.3716
17	1.1033	-0.1182	-0.6112	-0.0978	0.2728	0.5445	0.0456	0.0774	0.2199	-0.1374	-0.2161	-0.1785	0.1727	-0.1992	-0.0002	0.6471	0.0575	0.0295	0.4356	0.0247	0.3448	47.4433	-22.7958	-28.8679
18	0.1472	-0.1257	0.0132	0.1355	0.0692	0.1347	-0.8092	-0.7789	-0.4013	-0.2081	0.8129	-0.3535	0.8533	0.0954	-0.0002	1.0473	0.124	-0.0065	0.8543	0.0664	0.6976	58.9615	-47.2717	-21.57
19	0.0369	-0.0054	0.0248	0.0439	-0.0436	0.0359	0.2916	-0.7007	0.5541	0.057	-0.21	0.3902	0.2143	0.63	-0.0007	0.9473	0.104	0.0489	0.6864	-0.1426	0.6467	61.8401	-48.2082	-25.646
20	0.5014	-0.06	0.1105	0.4098	0.3833	0.3587	0.0729	0.1206	0.0199	0.0166	-0.129	-0.0269	0.1908	0.1414	-0.0001	0.4667	0.0137	-0.0064	0.3999	0.0152	0.425	50.2995	-34.3619	-17.3279
21	0.135	0.0713	0.327	0.9287	0.3957	0.677	0.2071	-0.1642	-0.0023	0.1783	-0.0886	-0.108	-0.1373	0.3592	-0.0001	0.4857	-0.095	-0.0377	0.5684	0.0244	0.5243	59.8402	-21.1656	-4.2215
22	0.7751	-0.3074	0.275	0.0265	0.2056	0.3751	0.6344	0.2775	-0.4696	-0.0015	-0.5532	-0.0097	-0.3346	-0.1023	-0	0.4986	0.0487	0.0391	0.4167	0.0079	0.4281	55.0658	-33.6319	-8.7642
23	0.2506	-0.1921	-0.2267	0.1005	0.2048	0.4778	-0.4949	-0.243	-0.1813	0.0494	-0.0858	-0.0497	0.2063	0.0586	0.0007	0.6924	-0.0455	-0.0271	0.6661	0.0018	0.5114	45.8297	-25.8877	12.5789
24	0.8847	-0.5644	-0.8752	0.2905	0.392	0.9043	0.1381	-0.0552	0.0266	-0.0089	0.0123	-0.0252	-0.0984	0.3156	-0	0.5472	-0.0445	-0.0403	0.4963	0.0473	0.4415	56.1896	-25.1773	6.5175
25	0.6517	0.0008	0.5371	0.1072	-0.7841	0.971	0.047	-0.7918	0.1515	-0.1246	0.0499	0.0934	0.4888	0.088	0.0076	0.6627	0.0186	-0.0223	0.537	0.0693	0.5187	46.2803	-32.9437	-4.7573
26	0.3284	-0.1117	0.3161	0.7483	-0.1221	0.6512	-0.0499	-0.0831	-0.1318	-0.0297	-0.0732	-0.1828	0.5504	0.2511	0.0002	0.4996	0.0338	0.0138	0.4809	0.0616	0.4618	59.1106	-34.9074	-10.0392

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 56:73)	A	56 - 73
2	X-RAY DIFFRACTION	2	(chain A and resid 74:88)	A	74 - 88
3	X-RAY DIFFRACTION	3	(chain A and resid 89:117)	A	89 - 117
4	X-RAY DIFFRACTION	4	(chain A and resid 118:146)	A	118 - 146
5	X-RAY DIFFRACTION	5	(chain A and resid 147:151)	A	147 - 151
6	X-RAY DIFFRACTION	6	(chain A and resid 152:159)	A	152 - 159
7	X-RAY DIFFRACTION	7	(chain A and resid 160:222)	A	160 - 222
8	X-RAY DIFFRACTION	8	(chain A and resid 223:263)	A	223 - 263
9	X-RAY DIFFRACTION	9	(chain A and resid 264:284)	A	264 - 284
10	X-RAY DIFFRACTION	10	(chain A and resid 285:300)	A	285 - 300
11	X-RAY DIFFRACTION	11	(chain A and resid 301:348)	A	301 - 348
12	X-RAY DIFFRACTION	12	(chain A and resid 349:367)	A	349 - 367
13	X-RAY DIFFRACTION	13	(chain A and resid 368:414)	A	368 - 414
14	X-RAY DIFFRACTION	14	(chain B and resid 56:73)	B	56 - 73
15	X-RAY DIFFRACTION	15	(chain B and resid 74:88)	B	74 - 88
16	X-RAY DIFFRACTION	16	(chain B and resid 89:117)	B	89 - 117
17	X-RAY DIFFRACTION	17	(chain B and resid 118:146)	B	118 - 146
18	X-RAY DIFFRACTION	18	(chain B and resid 147:151)	B	147 - 151
19	X-RAY DIFFRACTION	19	(chain B and resid 152:159)	B	152 - 159
20	X-RAY DIFFRACTION	20	(chain B and resid 160:222)	B	160 - 222
21	X-RAY DIFFRACTION	21	(chain B and resid 223:263)	B	223 - 263
22	X-RAY DIFFRACTION	22	(chain B and resid 264:284)	B	264 - 284
23	X-RAY DIFFRACTION	23	(chain B and resid 285:300)	B	285 - 300
24	X-RAY DIFFRACTION	24	(chain B and resid 301:348)	B	301 - 348
25	X-RAY DIFFRACTION	25	(chain B and resid 349:367)	B	349 - 367
26	X-RAY DIFFRACTION	26	(chain B and resid 368:414)	B	368 - 414

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