PDB-9f1o: Crystal structure of the DyP-type peroxidase PROSS variant from P...

ID or keywords:

Entry

Database: PDB / ID: 9f1o

Title

Crystal structure of the DyP-type peroxidase PROSS variant from Pseudomonas putida

Components

Dyp-type peroxidase PROSS variant

Keywords

OXIDOREDUCTASE / Protein Stability / Protein Engineering / Computational Engineering / DyPs

Function / homology

PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE

Function and homology information

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Constanca, L. / Borges, P.T. / Frazao, C. / Martins, L.O.

Funding support

Portugal, 2items

Citation

Journal: To Be Published
Title: One-step Computational Design of Hyperthermostable Bacterial DyP-type peroxidases
Authors: Silva, D. / Rodrigues, C.F. / Lorena, C. / Frazao, C. / Borges, P.T. / Martins, L.O.

History

Deposition	Apr 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9f1o.cif.gz	234.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9f1o.ent.gz	191.8 KB	Display	PDB format
PDBx/mmJSON format	9f1o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9f1o_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9f1o_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9f1o_validation.xml.gz	28.1 KB	Display
Data in CIF	9f1o_validation.cif.gz	37.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f1/9f1o ftp://data.pdbj.org/pub/pdb/validation_reports/f1/9f1o	HTTPS FTP

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Related structure data

Related structure data	9f1qC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: Dyp-type peroxidase PROSS variant

B: Dyp-type peroxidase PROSS variant

hetero molecules

64.7 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)	49.974, 84.812, 128.276
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Dyp-type peroxidase PROSS variant Mass: 31615.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-OXY / OXYGEN MOLECULE Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O₂
#3: 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
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.02 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion Details: 0.2 M calcium chloride dihydrate, 0.1 M MES pH 6.0 and 20 % (w/v) PEG 6000

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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 PILATUS3 X 6M / Detector: PIXEL / Date: May 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 2.1→70.75 Å / Num. obs: 32011 / % possible obs: 98.1 % / Redundancy: 3.1 % / R_pim(I) all: 0.0589 / Net I/σ(I): 9.72
Reflection shell	Resolution: 2.1→2.2 Å / Num. unique obs: 4971 / R_pim(I) all: 0.3214

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
PHASER		phasing
autoPROC		data reduction
autoPROC		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→70.75 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.22 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2291	1998	6.24 %
R_work	0.1935	-	-
obs	0.1957	32006	98.13 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→70.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4213	0	94	262	4569

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4421
X-RAY DIFFRACTION	f_angle_d	0.65	6031
X-RAY DIFFRACTION	f_dihedral_angle_d	13.545	1581
X-RAY DIFFRACTION	f_chiral_restr	0.042	623
X-RAY DIFFRACTION	f_plane_restr	0.007	802

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 (%)
2.1-2.15	0.2975	134	0.2765	2005	X-RAY DIFFRACTION	94
2.15-2.21	0.2831	140	0.243	2097	X-RAY DIFFRACTION	98
2.21-2.28	0.2777	141	0.2348	2129	X-RAY DIFFRACTION	99
2.28-2.35	0.2711	142	0.2312	2121	X-RAY DIFFRACTION	99
2.35-2.43	0.2669	141	0.2123	2125	X-RAY DIFFRACTION	99
2.43-2.53	0.2823	141	0.2138	2135	X-RAY DIFFRACTION	99
2.53-2.65	0.2502	143	0.2283	2146	X-RAY DIFFRACTION	99
2.65-2.79	0.262	141	0.221	2138	X-RAY DIFFRACTION	98
2.79-2.96	0.2553	144	0.219	2140	X-RAY DIFFRACTION	99
2.96-3.19	0.2557	141	0.2025	2128	X-RAY DIFFRACTION	98
3.19-3.51	0.2268	145	0.1839	2173	X-RAY DIFFRACTION	99
3.51-4.02	0.1942	144	0.163	2153	X-RAY DIFFRACTION	98
4.02-5.06	0.17	147	0.1484	2214	X-RAY DIFFRACTION	99
5.06-70.75	0.2197	154	0.1935	2304	X-RAY DIFFRACTION	98

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	3.1433	2.4859	2.8584	4.5787	4.2916	4.1744	-0.1336	-0.8024	-0.2889	0.6237	-0.065	1.1384	0.581	-0.2271	0.2062	0.3862	-0.0717	0.0373	0.4679	-0.0465	0.3481	27.8845	39.141	99.2098
2	2.2235	0.5427	0.7235	2.5589	2.0795	1.6307	0.1841	-0.2407	-0.2654	0.4253	-0.2935	-0.0283	0.4925	-0.0777	0.1076	0.3058	-0.021	0.0217	0.3669	0.0056	0.4276	26.6078	32.4386	88.9667
3	2.2336	-1.1455	-1.45	5.3745	5.4047	5.6562	-0.816	0.4347	0.3579	-1.1488	0.3041	1.5896	-0.5027	0.3537	0.5496	0.5567	0.0169	-0.078	0.4625	0.0009	0.6024	21.9696	52.25	74.6422
4	3.9902	0.3973	0.866	1.1021	0.2369	2.0509	0.0966	-0.442	0.2092	0.2658	-0.2282	0.5659	-0.1656	-0.2937	0.0164	0.2619	0.0538	0.0652	0.2886	-0.1192	0.4336	20.864	44.8399	88.2867
5	6.1294	1.747	2.8277	3.4465	3.5996	5.0861	-0.0516	0.5011	-0.0629	-0.041	0.3047	-0.7023	-0.6138	0.687	-0.2421	0.3972	0.014	0.0268	0.2186	0.0175	0.4242	31.6774	56.0246	83.7484
6	4.0411	-3.4909	-0.7629	3.0233	0.3956	0.5059	0.2401	0.2435	0.27	-0.1058	-0.2089	-0.204	-0.1505	0.0746	-0.0412	0.3001	-0.0206	-0.0022	0.2711	-0.01	0.3188	42.3511	42.4306	81.1242
7	6.1302	3.0448	0.6908	5.1087	-0.4778	1.4844	-0.0879	0.1947	-0.5018	-0.1217	-0.0343	0.0109	0.1686	-0.4909	0.1233	0.3112	-0.0194	0.093	0.4417	-0.0844	0.5048	20.2984	32.1874	86.0469
8	2.344	-1.0177	0.5355	5.9255	-0.8555	3.4893	0.0113	0.5534	-0.2504	-0.0602	-0.1475	0.4362	-0.0081	-0.1867	0.1022	0.2263	-0.0149	-0.0196	0.3761	-0.0172	0.4246	22.8195	37.7185	78.6836
9	0.6546	-1.7437	0.5295	9.255	3.9396	6.8458	0.6169	-1.2995	0.9174	0.6481	0.6126	-2.2216	-0.2819	0.4594	-1.1568	0.8296	-0.1049	-0.0199	1.0533	0.2496	1.4265	38.9175	20.4789	93.1015
10	3.8992	-4.2604	-5.1814	4.7642	5.5934	6.8876	-0.6499	-0.0488	-0.7217	1.5878	0.5724	0.311	2.8945	0.8373	-0.1696	0.6788	0.1067	0.0328	0.6791	-0.0781	0.4167	39.2685	31.8384	104.4058
11	8.6611	-5.9338	-0.6608	5.5085	-2.2737	6.5105	-0.3766	-0.2476	0.6887	0.7934	0.122	-1.1575	-0.3672	0.1951	0.2166	0.3654	-0.0675	-0.0272	0.4061	-0.099	0.3121	36.5191	43.0483	102.3093
12	5.5398	-2.5166	-2.4845	4.0103	4.0966	5.0478	-0.1587	-0.0502	-0.2368	0.0461	0.2366	0.1357	0.0098	0.5685	-0.0715	0.2351	-0.0049	-0.0003	0.2715	0.0374	0.1925	37.5027	34.6976	86.2678
13	8.0111	-1.5684	3.041	9.7512	0.567	8.4513	0.5425	0.0789	-0.9065	0.5346	-0.5902	0.0214	1.3916	0.1947	0.095	0.4737	-0.0906	0.0509	0.5539	-0.0526	0.6559	49.1383	15.5066	85.3804
14	6.5832	-2.1116	0.8441	8.5044	-1.4743	5.3013	0.7706	-3.3258	0.5298	2.4328	-1.4797	-0.8272	1.8612	-0.3349	0.7035	0.9738	-0.3499	0.0207	1.2671	-0.0128	0.6735	49.7831	16.3725	97.8238
15	6.464	-2.9832	-3.0484	4.0203	5.8572	8.9718	-0.2594	-0.7042	-0.4255	1.0502	0.3169	-0.4429	0.4919	-0.084	-0.1272	0.3353	-0.004	-0.0249	0.4413	0.0743	0.4913	54.5218	25.8307	92.1531
16	4.0851	2.4655	3.2437	8.4157	0.4248	3.271	0.4139	-1.9879	-1.2745	1.2399	-0.4239	-0.8709	-0.1516	-0.4099	-0.0767	0.5403	0.0176	-0.1067	0.7243	-0.0459	0.5017	52.3359	35.7565	98.9471
17	2.4803	0.0879	-1.479	3.5174	1.5462	4.9686	0.077	-0.3634	-0.2409	0.3523	-0.0705	-0.138	0.3165	0.0542	-0.0631	0.2155	0.062	-0.0219	0.2305	0.0225	0.2627	37.5274	29.59	88.452
18	4.0677	-0.7667	-1.4278	2.075	0.8379	1.6534	0.0979	-0.2208	0.0134	0.1301	-0.1432	-0.1973	-0.1154	0.2512	0.0153	0.2856	-0.0451	-0.0102	0.3646	-0.0039	0.2868	48.3725	35.8223	88.4017
19	2.8383	1.7054	-0.0125	1.9574	-0.0213	3.2267	0.1176	-0.044	0.2635	0.2253	-0.1801	0.2174	-0.2519	-0.1732	-0.0842	0.2153	-0.0153	0.0227	0.2048	0.0164	0.2321	33.5125	39.5075	88.6513
20	4.8105	-1.1364	1.2354	4.1901	3.6891	4.3167	0.5197	0.1919	0.4505	1.0591	0.755	-0.1567	-2.3427	-0.494	-0.3098	0.7117	0.1061	0.2817	0.4453	-0.0823	0.5387	25.669	56.1809	91.201
21	3.0191	-0.1501	-0.0041	2.1119	-1.154	0.6101	-0.103	0.3565	0.1489	-0.2923	0.1678	-0.0322	-0.0662	-0.1716	-0.0452	0.3569	-0.0254	-0.0131	0.3671	-0.0012	0.2882	45.7886	35.3381	53.9399
22	9.3476	-2.7944	-6.4361	9.4984	3.2565	4.9402	-0.5202	-0.8713	-0.2014	0.5314	0.3205	-0.1941	0.1917	0.1631	0.2663	0.3467	0.0677	-0.0411	0.4508	0.024	0.3019	56.888	23.3766	71.7473
23	1.4423	-1.4281	2.0651	4.4803	-2.7258	4.7978	0.1376	0.3781	0.0497	-0.8884	-0.5436	-0.5091	0.8951	0.3469	0.5833	0.2949	0.0362	0.0749	0.3928	0.0314	0.306	56.1253	26.1729	56.2448
24	7.9489	1.5069	4.2753	2.4478	-0.5738	3.4509	0.1745	0.2289	0.0114	0.1427	-0.1744	0.1337	1.0048	0.4648	0.0311	0.2054	0.0444	0.0305	0.1612	0.016	0.2124	53.5083	34.2485	63.4313
25	6.4863	0.7904	2.9329	0.1517	-0.2	7.5258	-0.3054	-0.3795	0.468	0.1038	-0.4925	-2.0133	-1.1272	0.1908	0.4244	0.3142	-0.0545	-0.0199	0.4585	0.1643	0.5884	62.2865	38.6334	69.8551
26	1.3372	-0.7562	-0.2538	1.495	-0.2367	0.454	-0.0428	-0.0103	0.145	0.0254	0.0788	0.0363	-0.098	-0.0162	-0.0687	0.2517	-0.0194	-0.0234	0.2699	0.0065	0.2208	43.8859	39.4349	64.643
27	6.1925	-4.4474	3.5306	4.8784	-4.7191	4.9447	0.1921	2.0059	-0.1325	-1.248	0.0624	-0.0868	0.6361	-0.0524	-0.3708	0.4145	-0.0867	0.0574	0.4733	-0.027	0.3372	42.7242	22.3023	53.6688
28	5.6582	-1.2134	6.6883	1.4538	-2.9076	9.6643	0.4256	-0.0606	-1.4653	-0.6961	-0.1331	0.1641	1.4999	-0.6096	0.1389	0.3768	-0.0007	0.0299	0.2131	-0.0187	0.2786	49.1202	21.0431	61.9746
29	4.271	-0.2481	0.6539	1.0259	1.1574	2.3185	0.3928	0.6203	-0.7281	-0.2369	-0.2144	0.4539	-0.0407	0.0244	-0.1696	0.2819	0.0468	-0.0092	0.4048	0.0088	0.3181	40.5236	31.0142	60.5861
30	2.3326	-1.3578	2.4769	7.4359	-1.8429	9.4752	-0.231	0.6271	1.1217	-0.6461	0.0222	-0.2967	-0.8398	-0.3417	0.2289	0.4584	-0.0132	0.0145	0.3402	0.0576	0.364	48.7736	51.2445	49.0357
31	3.5687	-2.4131	0.961	3.6645	0.2634	3.9416	0.4722	-0.4216	0.8605	0.2425	-0.2142	0.8171	-0.4078	-0.5806	0.1122	0.2142	0.0577	0.0378	0.1886	0.0327	0.3244	35.9378	43.5424	61.6897
32	2.2559	2.4082	-0.2675	2.0042	-7.0123	6.0652	-0.1272	0.2407	-0.8374	0.4988	1.6107	3.5134	-0.3078	-2.3085	-1.0736	0.5059	-0.0273	0.0922	0.7923	0.2427	1.2825	17.2287	52.9615	59.5038
33	3.9245	-0.2867	5.39	9.4495	0.222	7.4927	-0.341	0.3929	1.0756	-0.9034	0.0565	1.1941	-0.2617	-0.3977	0.2482	0.7233	0.0597	-0.0259	0.6727	0.1395	0.6575	25.806	56.8642	55.9155
34	3.8115	0.549	-3.0868	8.7627	0.6788	3.7156	0.1368	0.9362	1.1619	-0.7487	0.1351	-0.0906	-0.392	-0.5786	-0.2441	0.5909	0.0443	0.0145	0.565	0.0782	0.5622	34.1699	60.7963	58.6907
35	5.3628	-0.7194	4.4043	5.408	0.5939	7.1062	0.7532	0.3471	0.8966	0.2395	-0.3011	-0.2657	-0.6716	0.1481	0.0065	0.449	-0.0824	0.1485	0.3404	0.0688	0.5339	45.3597	53.9867	55.663
36	7.3692	2.2295	-1.1283	3.9925	0.4877	1.6182	-0.0292	-0.1202	-0.1589	-0.1621	0.1094	0.2976	0.0753	-0.3283	-0.069	0.2282	-0.0185	-0.0217	0.2786	0.0661	0.2738	34.7574	38.5006	59.3958
37	9.1132	-3.8686	-4.164	7.8372	1.4795	5.2481	-0.1487	0.0273	0.5174	-0.1058	0.2809	-0.1791	-0.5531	0.4822	-0.1577	0.3899	-0.0742	0.0014	0.3339	-0.025	0.34	46.0398	52.6553	63.9313
38	4.9448	-0.9895	1.48	6.7025	-0.1658	5.8313	-0.1078	0.1151	0.0198	0.1059	0.3656	0.2648	-0.6065	0.2633	-0.2203	0.4882	0.0533	0.0244	0.4181	-0.0303	0.3949	34.4458	56.4027	68.3611
39	6.0886	-1.6592	-1.3196	3.689	-0.0646	2.8438	0.2508	-0.0764	0.0799	-0.1373	-0.1418	-0.2128	-0.3064	0.2907	-0.0971	0.3538	-0.0265	-0.0084	0.233	0.0232	0.2491	47.5135	40.0768	60.6271
40	6.4366	4.6327	-3.9536	9.448	-2.2112	3.2498	0.3222	-0.6219	0.9902	0.7273	-0.6297	-1.5048	-0.3066	0.5854	0.3635	0.2142	0.0388	0.0445	0.4582	0.1084	0.6017	64.8466	34.8751	62.9598

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:7)
2	X-RAY DIFFRACTION	2	(chain A and resid 8:22)
3	X-RAY DIFFRACTION	3	(chain A and resid 23:28)
4	X-RAY DIFFRACTION	4	(chain A and resid 29:52)
5	X-RAY DIFFRACTION	5	(chain A and resid 53:60)
6	X-RAY DIFFRACTION	6	(chain A and resid 61:82)
7	X-RAY DIFFRACTION	7	(chain A and resid 83:102)
8	X-RAY DIFFRACTION	8	(chain A and resid 103:119)
9	X-RAY DIFFRACTION	9	(chain A and resid 120:134)
10	X-RAY DIFFRACTION	10	(chain A and resid 135:141)
11	X-RAY DIFFRACTION	11	(chain A and resid 142:150)
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39	X-RAY DIFFRACTION	39	(chain B and resid 259:280)
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