PDB-8ck9: DyP-type peroxidase from Thermobifida halotolerans

ID or keywords:

Entry

Database: PDB / ID: 8ck9

Title

DyP-type peroxidase from Thermobifida halotolerans

Components

Peroxidase

Keywords

OXIDOREDUCTASE / Heme / peroxidase / DyP / ferredoxin-like fold

Function / homology

Function and homology information

peroxidase activity / heme binding
Similarity search - Function

Biological species

Thermobifida halotolerans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Pupart, H. / Lukk, T.

Funding support

Estonia, 1items

Citation

Journal: Arch.Biochem.Biophys. / Year: 2024
Title: Dye-decolorizing peroxidase of Thermobifida halotolerance displays complex kinetics with both substrate inhibition and apparent positive cooperativity.
Authors: Pupart, H. / Lukk, T. / Valjamae, P.

History

Deposition	Feb 14, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ck9.cif.gz	168.5 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	8ck9.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8ck9_validation.pdf.gz	822.1 KB	Display	wwPDB validaton report
Full document	8ck9_full_validation.pdf.gz	823.9 KB	Display
Data in XML	8ck9_validation.xml.gz	19.3 KB	Display
Data in CIF	8ck9_validation.cif.gz	30 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ck/8ck9 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/8ck9	HTTPS FTP

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Related structure data

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	#220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2)

Deposited unit

A: Peroxidase

hetero molecules

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

1

A: Peroxidase

hetero molecules

A: Peroxidase

hetero molecules

defined by author&software
Evidence: gel filtration
92.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.358, 78.370, 135.649
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-862- HOH
2	1	A-872- HOH
3	1	A-896- HOH

#1: Protein	Peroxidase Mass: 45409.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The model contains bound heme (HEM) and nitrate (NO3) Source: (gene. exp.) Thermobifida halotolerans (bacteria) / Gene: NI17_20570 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A399FZ67
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.06 Å³/Da / Density % sol: 40.28 %
Crystal grow	Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein concentration was at 15 mg/mL in Tris-HCl (20 mM, pH 7.5); mother liquor was 0.2 M sodium nitrate, 0.1 M Bis-Tris propane, pH 7.5, 20% (w/v) PEG3350.

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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: Oct 26, 2021
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 1.6→29.61 Å / Num. obs: 49674 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.993 / R_merge(I) obs: 0.1 / R_pim(I) all: 0.041 / R_rim(I) all: 0.108 / Χ²: 0.91 / Net I/σ(I): 11.5 / Num. measured all: 338025
Reflection shell	Resolution: 1.6→1.63 Å / % possible obs: 99.8 % / Redundancy: 6.4 % / R_merge(I) obs: 0.277 / Num. measured all: 15285 / Num. unique obs: 2387 / CC_1/2: 0.954 / R_pim(I) all: 0.118 / R_rim(I) all: 0.302 / Χ²: 0.52 / Net I/σ(I) obs: 4.7

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→29.61 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1874	2473	4.98 %
R_work	0.1569	-	-
obs	0.1584	49628	99.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→29.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2830	0	47	423	3300

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2983
X-RAY DIFFRACTION	f_angle_d	0.829	4081
X-RAY DIFFRACTION	f_dihedral_angle_d	12.779	1091
X-RAY DIFFRACTION	f_chiral_restr	0.05	438
X-RAY DIFFRACTION	f_plane_restr	0.008	553

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 (%)
1.6-1.63	0.1976	132	0.1665	2567	X-RAY DIFFRACTION	100
1.63-1.66	0.2007	149	0.1596	2561	X-RAY DIFFRACTION	100
1.66-1.7	0.2084	131	0.1625	2620	X-RAY DIFFRACTION	100
1.7-1.74	0.1857	141	0.1562	2545	X-RAY DIFFRACTION	99
1.74-1.78	0.2036	123	0.1652	2609	X-RAY DIFFRACTION	100
1.78-1.83	0.2167	147	0.1617	2581	X-RAY DIFFRACTION	100
1.83-1.89	0.2042	145	0.1559	2619	X-RAY DIFFRACTION	100
1.89-1.95	0.1791	133	0.151	2618	X-RAY DIFFRACTION	100
1.95-2.02	0.1765	121	0.155	2594	X-RAY DIFFRACTION	100
2.02-2.1	0.1936	146	0.154	2600	X-RAY DIFFRACTION	100
2.1-2.19	0.1576	145	0.1565	2605	X-RAY DIFFRACTION	99
2.19-2.31	0.1982	143	0.1577	2603	X-RAY DIFFRACTION	100
2.31-2.45	0.2065	145	0.1585	2610	X-RAY DIFFRACTION	100
2.45-2.64	0.1756	134	0.1629	2650	X-RAY DIFFRACTION	100
2.64-2.91	0.198	118	0.1692	2653	X-RAY DIFFRACTION	100
2.91-3.33	0.1915	124	0.1642	2672	X-RAY DIFFRACTION	100
3.33-4.19	0.1681	162	0.141	2653	X-RAY DIFFRACTION	100
4.19-29.61	0.1902	134	0.1551	2795	X-RAY DIFFRACTION	100

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	0.0974	0.0878	0.1278	0.0713	0.119	0.1623	0.0507	0.065	-0.1459	-0.0819	-0.0397	-0.0742	0.4299	0.0062	-0.0037	0.3535	0.0289	0.0134	0.1548	0.0081	0.2234	0.1356	2.8995	-22.0577
2	0.2284	0.0993	-0.006	0.0525	0.0409	0.1383	-0.0507	0.0122	0.0551	-0.0006	0.0351	0.0106	-0.0017	-0.0186	-0.0082	0.1177	0.0291	0.0029	0.0724	0.006	0.1175	-3.8409	24.2246	-16.9219
3	0.1024	-0.0355	0.093	0.1359	-0.1034	0.1582	0.0059	-0.05	0.0114	0.0916	-0.1509	0.0776	0.1783	-0.2128	-0.0064	0.1383	-0.013	0.0153	0.0965	-0.0141	0.1491	-13.0176	20.7648	-10.8603
4	0.2081	-0.15	-0.0475	0.1579	-0.0985	0.2762	-0.044	-0.0419	0.0003	0.0264	0.0394	0.0379	0.0363	-0.0085	-0.0014	0.0862	0.0097	-0.0011	0.0872	-0.0031	0.1081	-4.9142	20.6067	-13.3465
5	0.2256	-0.0649	-0.0411	0.1234	0.0162	0.1293	-0.0348	0.0726	0.0818	-0.0836	-0.0017	-0.002	-0.0504	-0.007	-0.0221	0.1117	0.0034	0.0012	0.0646	0.0182	0.121	6.0317	29.166	-19.0137
6	0.1048	0.027	0.1169	0.0548	0.024	0.1211	-0.0417	0.0654	0.0525	-0.1272	-0.0125	0.0517	-0.0125	-0.0743	-0	0.1218	0.0179	-0.0173	0.1106	0.0061	0.1359	-7.8398	23.8744	-23.2295
7	0.1887	0.0004	0.0723	0.0274	0.0667	0.1416	-0.0736	-0.0456	-0.2555	-0.0405	0.133	0.0311	0.1051	0.0039	0.0138	0.1485	0.0232	0.011	0.1295	0.0582	0.1737	13.4143	8.975	-22.4006
8	0.2944	0.0999	0.0131	0.1509	0.099	0.0713	-0.0558	-0.1418	0.032	0.0246	-0.0437	-0.0297	0.061	0.1356	-0.0259	0.0912	0.0223	0.0116	0.1214	0.037	0.0812	7.1218	22.1357	-6.9243
9	0.2655	0.2066	0.0509	0.2608	0.1917	0.2121	-0.0287	0.2562	-0.0869	-0.0951	0.0744	-0.03	0.0305	0.156	0.0078	0.1063	-0.0056	0.0151	0.1859	0.004	0.0991	26.3939	14.966	-30.4894
10	0.0562	-0.0477	0.0223	0.0268	-0.0125	0.0859	-0.0564	-0.1352	0.0908	0.0417	0.0499	-0.0334	-0.0433	0.2223	-0.0016	0.0733	0.0011	0.0033	0.1756	0.0034	0.0832	33.759	18.1794	-19.8977
11	0.2469	0.0609	-0.0557	0.1291	0.1398	0.1721	-0.1038	0.0917	0.0232	-0.0803	0.0431	0.0055	-0.1729	0.1146	-0.0088	0.1431	-0.026	-0.0173	0.1187	0.048	0.0984	11.3157	23.8764	-26.2175
12	0.1121	-0.0401	-0.0881	0.1026	0.0387	0.0675	-0.043	-0.0855	0.0773	0.0304	0.0473	0.0219	-0.093	0.0491	0.0179	0.0943	-0.0094	0.0025	0.1179	0.0203	0.0972	17.1239	24.4507	-15.2967
13	0.2897	0.0846	0.2201	0.1639	0.1889	0.2629	0.021	-0.058	0.1028	0.021	0.0005	0.0257	0.0042	-0.0434	-0.024	0.0879	-0.0007	0.0171	0.0847	0.0352	0.0812	3.5371	23.4884	-12.7328

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 18 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 61 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 86 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 87 through 126 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 127 through 154 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 155 through 182 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 183 through 220 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 221 through 246 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 247 through 283 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 284 through 308 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 309 through 332 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 333 through 360 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 361 through 391 )

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