PDB-8re3: Crystal Structure determination of Dye-decolorizing Peroxidase (D...

ID or keywords:

Entry

Database: PDB / ID: 8re3

Title

Crystal Structure determination of Dye-decolorizing Peroxidase (DyP) mutant M190G from Deinoccoccus radiodurans

Components

Peroxidase, putative

Keywords

STRUCTURAL PROTEIN / Peroxidase / Heme / Hydrogen Peroxide / D.radiodurans

Function / homology

Function and homology information

peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Deinococcus radiodurans (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.51 Å

Authors

Salgueiro, B.A. / Frade, K. / Frazao, C. / Matias, P. / Moe, E.

Funding support

Portugal, 6items

Organization	Grant number	Country
Foundation for Science and Technology (FCT)	PTDC/BBBEBB/0122/2014	Portugal
Foundation for Science and Technology (FCT)	SFRH/BPD/97493/2013	Portugal
Foundation for Science and Technology (FCT)	COVID/BD/152598/2022	Portugal
Foundation for Science and Technology (FCT)	UIDB/04612/2020	Portugal
Foundation for Science and Technology (FCT)	UIDP/04612/2020	Portugal
Foundation for Science and Technology (FCT)	LA/P/0087/2020	Portugal

Citation

Journal: Molecules / Year: 2024
Title: Biochemical, Biophysical, and Structural Analysis of an Unusual DyP from the Extremophile Deinococcus radiodurans.
Authors: Frade, K. / Silveira, C.M. / Salgueiro, B.A. / Mendes, S. / Martins, L.O. / Frazao, C. / Todorovic, S. / Moe, E.

History

Deposition	Dec 10, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 31, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8re3.cif.gz	522 KB	Display	PDBx/mmCIF format
PDB format	pdb8re3.ent.gz	436.4 KB	Display	PDB format
PDBx/mmJSON format	8re3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8re3_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8re3_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8re3_validation.xml.gz	38.7 KB	Display
Data in CIF	8re3_validation.cif.gz	57.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/re/8re3 ftp://data.pdbj.org/pub/pdb/validation_reports/re/8re3	HTTPS FTP

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Related structure data

Related structure data	8re2C C: citing same article (ref.)
Similar structure data	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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #57 - Sep 2004 Catalase similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Peroxidase, putative

B: Peroxidase, putative

hetero molecules

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

1

A: Peroxidase, putative

hetero molecules

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

2

B: Peroxidase, putative

hetero molecules

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

Unit cell

Length a, b, c (Å)	82.090, 97.697, 116.037
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Peroxidase, putative Mass: 49722.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: DR_A0145 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL / Variant (production host): star / References: UniProt: Q9RZ08

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Non-polymers , 5 types, 639 molecules

#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: Chemical	ChemComp-OH / HYDROXIDE ION Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 629 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.32 Å³/Da / Density % sol: 46.96 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion Details: 0.06M Divalent (0.3M Magnesium Cloride hexahydrate, 0.3M Calcium Cloride dihydrate), 0.1M buffer (1M Tris pH8.5, BICINE), 50% v/v Precipitant (40% v/v PEG 500 MME, 20% w/v PEG 20000)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 7, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.51→74.74 Å / Num. obs: 188084 / % possible obs: 93.4 % / Redundancy: 5.7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.071 / R_pim(I) all: 0.032 / R_rim(I) all: 0.078 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.511→1.655 Å / R_merge(I) obs: 0.849 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4914 / CC_1/2: 0.784 / R_pim(I) all: 0.408 / R_rim(I) all: 0.946

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.51→74.74 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.6 / Phase error: 26.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1948	9282	4.94 %
R_work	0.1668	-	-
obs	0.1682	188084	66.52 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.51→74.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7104	0	8	629	7741

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	7338
X-RAY DIFFRACTION	f_angle_d	1.05	9968
X-RAY DIFFRACTION	f_dihedral_angle_d	13.83	2746
X-RAY DIFFRACTION	f_chiral_restr	0.058	1023
X-RAY DIFFRACTION	f_plane_restr	0.012	1314

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 (%)
1.51-1.53	0.1871	2	0.3173	46	X-RAY DIFFRACTION	1
1.53-1.55	0.2244	15	0.3602	198	X-RAY DIFFRACTION	2
1.55-1.56	0.3206	31	0.3297	633	X-RAY DIFFRACTION	7
1.56-1.58	0.3863	45	0.3005	960	X-RAY DIFFRACTION	11
1.58-1.61	0.282	68	0.3011	1543	X-RAY DIFFRACTION	17
1.61-1.63	0.2533	105	0.2905	2146	X-RAY DIFFRACTION	24
1.63-1.65	0.2712	152	0.2638	2769	X-RAY DIFFRACTION	31
1.65-1.68	0.3458	177	0.2559	3399	X-RAY DIFFRACTION	38
1.68-1.7	0.2712	214	0.2501	4063	X-RAY DIFFRACTION	45
1.7-1.73	0.2566	232	0.2402	4543	X-RAY DIFFRACTION	51
1.73-1.76	0.2835	278	0.2329	4932	X-RAY DIFFRACTION	55
1.76-1.79	0.242	285	0.2316	5333	X-RAY DIFFRACTION	59
1.79-1.83	0.2666	292	0.228	5748	X-RAY DIFFRACTION	64
1.83-1.86	0.2647	347	0.2214	6215	X-RAY DIFFRACTION	70
1.86-1.9	0.2507	316	0.2203	6798	X-RAY DIFFRACTION	75
1.9-1.95	0.2482	389	0.2177	7196	X-RAY DIFFRACTION	81
1.95-2	0.2149	411	0.1948	7776	X-RAY DIFFRACTION	87
2-2.05	0.2198	405	0.1835	8260	X-RAY DIFFRACTION	92
2.05-2.11	0.2329	507	0.1737	8634	X-RAY DIFFRACTION	98
2.11-2.18	0.2071	427	0.1695	8858	X-RAY DIFFRACTION	99
2.18-2.26	0.2098	449	0.1626	8851	X-RAY DIFFRACTION	99
2.26-2.35	0.2014	483	0.1617	8784	X-RAY DIFFRACTION	98
2.35-2.45	0.181	424	0.1626	8935	X-RAY DIFFRACTION	99
2.45-2.58	0.1836	486	0.1646	8827	X-RAY DIFFRACTION	99
2.58-2.74	0.2067	395	0.1627	8929	X-RAY DIFFRACTION	99
2.74-2.96	0.1929	480	0.1562	8855	X-RAY DIFFRACTION	98
2.96-3.25	0.1796	516	0.1539	8846	X-RAY DIFFRACTION	99
3.25-3.73	0.1635	472	0.1438	8929	X-RAY DIFFRACTION	100
3.73-4.69	0.1501	421	0.126	8908	X-RAY DIFFRACTION	99
4.69-74.74	0.1756	458	0.1692	8888	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	0.3834	0.0485	-0.0723	0.7897	-0.1394	0.2206	-0.0913	-0.0187	-0.0472	0.3669	0.0395	0.1495	0.0526	-0.0366	-0.0357	0.1581	0.0133	-0.0224	0.1456	-0.0348	0.1496	13.7962	2.5473	19.3654
2	0.458	-0.0215	-0.0268	1.5076	-0.2183	0.5076	-0.0391	-0.0596	0.0921	0.16	0.0451	-0.0867	-0.0684	0.0252	0.0495	0.0949	0.0009	-0.0595	0.1366	-0.0418	0.1487	18.8641	12.2651	15.8694
3	0.3052	0.1742	-0.0946	0.6285	0.4528	0.4313	0.0561	0.0411	0.0474	-0.226	0.1124	-0.1972	-0.1914	0.0851	1.0551	0.051	-0.0321	-0.1477	0.1207	-0.0294	0.1586	23.1547	13.3602	5.7833
4	0.1472	-0.0091	0.0565	1.4398	-0.4091	0.1545	0.1164	0.278	-0.0814	-0.9864	-0.0739	-0.0119	0.178	-0.0143	-0.0675	0.4968	-0.0049	-0.1082	0.1983	-0.0367	0.0828	17.7958	7.8734	-11.8115
5	0.2774	0.1624	0.0209	0.7298	-0.2571	0.1482	-0.0164	0.1582	0.1025	-0.4934	0.0004	-0.1003	0.0149	0.0954	-0.0191	0.2094	-0.0126	-0.0198	0.1894	0.0025	0.2074	21.9922	11.8711	-1.1038
6	0.0989	0.0039	0.0548	0.4873	0.0589	0.0829	0.0216	0.1174	0.2267	-0.2746	-0.0076	-0.2556	-0.0531	0.0762	0.0043	0.1264	-0.0126	-0.0012	0.1695	0.0074	0.2553	25.9924	16.9604	2.9617
7	0.7245	-0.004	0.0863	0.0016	-0.0072	0.0144	0.0519	0.0672	0.2769	-0.5019	-0.0539	-0.124	-0.0912	0.0265	-0.0353	0.4194	-0.0323	0.0511	0.2222	0.0791	0.2688	26.8032	21.8706	-11.9325
8	0.2928	-0.0375	0.0281	0.5091	0.3221	0.1727	-0.0484	-0.0477	0.0938	0.0277	0.0475	-0.2482	0.0455	0.0613	0.1113	0.1531	-0.0078	-0.0611	0.1316	-0.0215	0.1632	22.7252	14.7648	13.5345
9	0.3973	0.021	0.0021	0.468	-0.1934	0.2204	-0.0826	0.0887	0.0717	-0.2152	0.1196	0.1182	-0.1135	-0.0393	0.0081	0.1575	-0.0007	-0.0258	0.142	0.0007	0.1103	13.337	45.9192	48.516
10	0.6763	0.158	-0.305	1.3805	-0.6256	0.7522	-0.0528	0.0407	-0.0609	-0.0772	0.0698	-0.0578	-0.0081	-0.0485	0.0061	0.0779	0.0019	-0.013	0.1406	-0.0155	0.1108	18.3794	36.5443	52.3418
11	0.2497	-0.196	-0.0588	0.5066	0.3371	0.2025	-0.0363	-0.0477	-0.0753	0.1275	-0.0093	-0.224	-0.0432	0.0595	0.013	0.0889	0.0011	-0.0428	0.1376	0.003	0.1228	22.3154	35.7419	62.3087
12	0.2002	0.1019	-0.1386	0.7239	-0.0256	0.149	0.2715	-0.3746	0.2276	0.8705	-0.1013	0.0516	-0.468	0.0357	0.1815	0.5778	-0.01	0.0236	0.2272	-0.0681	-0.2156	16.1165	41.0131	79.9797
13	0.1393	-0.2097	-0.0297	0.4083	-0.1175	0.1381	-0.0003	-0.1648	-0.0707	0.4249	-0.002	-0.0516	-0.2409	0.095	-0.0054	0.2044	-0.0331	-0.0781	0.1973	0.0067	0.1228	20.8063	36.9354	69.4995
14	0.0198	-0.0659	0.0194	0.2284	-0.1076	0.0861	0.0717	-0.068	-0.1758	0.2613	-0.0643	-0.2371	-0.0953	0.0422	0.0122	0.1208	-0.0097	-0.0748	0.1731	0.0284	0.197	24.9473	31.9269	65.5754
15	0.224	-0.0202	-0.0291	0.0033	-0.0013	0.0068	0.0953	-0.3101	-0.1838	0.4992	-0.1389	-0.0712	-0.0065	0.0304	-0.0709	0.3595	-0.0463	-0.1221	0.2811	0.065	0.1932	25.1939	27.0698	80.4561
16	0.3542	0.1072	0.0413	0.4619	0.2658	0.1376	-0.0482	0.0329	-0.1116	0.0207	-0.009	-0.2543	-0.0946	0.0724	-0.0263	0.0812	0.0172	-0.018	0.1164	0.0021	0.0989	21.8822	33.7162	54.9392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 73 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 74 through 217 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 218 through 263 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 264 through 325 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 326 through 361 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 362 through 402 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 403 through 424 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 425 through 457 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 13 through 73 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 74 through 217 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 218 through 263 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 264 through 325 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 326 through 361 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 362 through 402 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 403 through 424 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 425 through 457 )

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